WO2021257760A1

WO2021257760A1 - High throughput analysis and sorting apparatus and method

Info

Publication number: WO2021257760A1
Application number: PCT/US2021/037721
Authority: WO
Inventors: Michael IANNOTTI
Original assignee: Iannotti Michael
Priority date: 2020-06-19
Filing date: 2021-06-17
Publication date: 2021-12-23

Abstract

A device and method may be useful for analyzing and/or sorting selected biological material such as cells or other biological components. The process can include receiving by a mixing region a first mixture that includes target biological material bound to first separation entities from a first separation region. The mixing region may receive a second mixture that includes a cleaving entity linked to second separation entities. The cleaving entity may cleave a linker connected to the target biological material from the first separation entities. The first mixture and second mixture may be conveyed to a second separation region. At least one first fraction enriched for target biological material and at least one second fraction that is substantially devoid of the target biological material may be collected. An apparatus with two separation regions and a mixing region connected to an analysis and/or sorting device may support this method.

Description

HIGH THROUGHPUT ANALYSIS AND SORTING APPARATUS AND METHOD

BACKGROUND OF THE INVENTION

Field of the Invention

[0001] Methods, systems, and apparatuses are disclosed that analyze and separate target biological materials from background materials. The separated target biological materials are suitable for research and clinical applications.

Discussion of Related Art

[0002] The analysis and sorting of biological materials has a variety of applications in both clinical and laboratory' settings. Flow cytometry and other microfluidic sorting methods such as magnetic sorting can separate biological materials, such as cells. Cell separation can be used for cell-based research and therapeutics in which selected cells are administered to a patient. Ceil separation has been used in the context of blood transfusions, chimeric antigen receptor (CAR) T cell therapy, regulatory T cell production, human stem cell enrichment/therapy, and screening for a desired phenotype/genotype. In some configurations, cell separation can be used to isolate circulating tumor cells (CTCs) from patients for diagnostic and analytical purposes.

[0003] One example of a flow cytometry technique is fluorescence-activated cell sorting (FACS). In this technique, target ceils are labeled with a fluorophore and are present in a heterogeneous mixture of ceils that are not labeled. The heterogeneous mixture is passed through a fluidic channel in which the cells are focused into a single-file stream of ceils. The cells are streamed past a laser beam in the analysis and sorting device (e.g., flow cytometer), which causes excitation of the fluorophore on target cells and/or scatters light as it contacts the cell. If the emission of a fluorophore is detected, the target cell can be sent to a collection tube. The process of scanning and diverting cells can be controlled by a computer connected to the device. A modern flow cytometer may process, for example, several thousand cells per second. [0004] Column purification has been used for decades to separate desired biological materials such as cells and/or molecules (e.g., proteins or nucleic acids) from undesired components. U.S. Pat. No. 9,885,032 discloses examples of column purification to separate components using magnetic-activated cell sorting (MACS), and also discloses methods involving sequential selection through application of more than one multiple magnetic field gradient. In U.S. Pat. No. 9,885,032, the second magnetic field gradient is applied to a mixture in which a labeled component from the first magnetic separation (using the first magnetic field gradient) has been removed. Ceil sorting systems have been developed that are significantly more efficient and accurate in sorting cells. U.S. Pat. No. 10,240,186 discloses microfluidic devices that can be used for the separation of cells or other biological materials of interest. The device can use a magnet to separate cells labeled with magnetic beads. The magnet may be incorporated into fluidic channels or removable. Additional configurations for the structure of microfluidic tubing are provided that are designed to trap the cells near the magnet. Patent 10,240,186 purports to address several deficiencies associated with current cell sorting techniques. It provides higher capture efficiency because the sample is passed near the source of a magnetic field due to the use of microfluidic channels. Furthermore, the microfluidic channels shorten run times. Patent 10,240,186 is incorporated herein by reference in its entirety .

[0005] Other examples of magnetic separation devices are provided in U.S. Pat. Nos. 8,727,132 and 7,713,752. U.S. Pat. App. Pub. No. 2017/0284922 discloses a magnetic separation process to separate cells displaying and/or secreting a protein of interest. U.S. Pat. No. 7,713,752 discloses a magnetic bead agglomerator for an automated enzyme-linked immunoassay (“ELISA”) process. U.S. Pat. No, 10,073,079 discloses how to capture particles within a flow of fluid. More examples of microfluidic devices and methods and use thereof are provided in U.S. Pat. App.

Pub. No. 2017/0268037 and International App. Pub. No. W02020/010471. U.S. Pat. No. 10,053,665 discloses a magnetic cell sorting system that uses a magnetic field to separate particles. International App. Pub. No. WO1996/031776 discloses multiparameter cell separation using releasable colloidal magnetic particles, in which blocking solution may be added to prevent reaction of residual release agent with the microparticles during subsequent separation steps. [0006] U.S. Pat. No. 10,073,079, as noted above, discloses a device for capturing particles in a flow and notes that combining magnetic nanobeads with fluid separation is difficult because the nanobeads possess a low inherent magnetic susceptibility. When a magnetic force is applied to the beads, they are incapable of overcoming the drag forces produced by even slowly flowing liquids. A common solution to this problem is the use of microfluidic channels, but this can require high-gradient magnetic fields that can be difficult to attain in portable or compact devices. U.S. Pat. No. 10,073,079 discloses a variety of structures shaped to reduce the flow' rate in a vicinity of a trapping surface to promote trapping of the particles.

[0007] Mair et al, “High-throughput genome-wide phenotypic screening via immunomagnetic cell sorting”, Nat Biotned. Eng.. Vol. 3, pp. 796-805, October 2019, screened cells for a loss-of- function phenotype. Mair et al. used microfluidic immunomagnetic cell sorting (MICS), in which magnetic guides deflect cells recognized by antibodies coupled to magnetic beads. In contrast to FACS, which requires sequential analysis and sorting of each cell, MICS simultaneously sorts a heterogeneous population of cells. Mair et al. demonstrated a genome-wide screen of 10^s cells in less than 1 hour. Mair et al. is incorporated herein by reference in its entirety.

[0008] Legut et al., “Immunomagnetic cell sorting”, NaL Biomed. Eng.. Vol. 3, pp. 759-760, October 2019, noted that MICS lacks some of the control over the sorting process that FACS can provide. FACS is also amenable to simultaneous multiplexing with different fluorescent labels for different targets, whereas MICS cannot simultaneously multiplex magnetic labels for different desirable targets.

[0009] There is a need for the ability to separate target biological materials that are suitable for research and clinical or therapeutic use from undesirable contaminants such as background biological materials. Currently, the above-described systems use a single separation method in which the target biological materials are separated from undesired components, but the method may be low throughput, may require introduction of a blocking solution, and/or may allow separating components such as beads to remain on the target. Consequently, they are restricted by the limitations of the individual separation method and can have impurities which w'ould not be desirable for clinical or therapeutic use. SUMMARY

[0010] At least the following embodiments are disclosed:

[0011] 1. An analysis and/or sorting system, comprising: a first separation region having at least one first inlet and at least one first outlet, wherein the first separation region comprises a first mixture, the first mixture comprising a first capture complex, which comprises a first separation entity linked via a first linker to a first binding entity bound to a target biological material; a mixing region comprising: at. least, one second inlet for receiving the first mixture from the at least one first, outlet of the first separation region and for receiving a second mixture comprising a cleaving entity jinked via a second linker to a second separation entity, wherein the cleaving entity cleaves the first linker of the first capture complex; and at least one second outlet, a second separation region having at least one third inlet and at least one third outlet, the at least one third inlet receiving material from the at least one second outlet of the mixing region; and an analysis and/or sorting device that separates a mixture from the at least one third outlet of the second separation region into at least one first fraction enriched for the target biological material and at least one second fraction that is substantially devoid of the target biological material.

[0012] 2. The analysis and/or sorting system of embodiment 1, wherein the first separation region and/or the second separation region comprises a magnet or an electromagnet, and wherein the first separation entity and the second separation entity are magnetic.

[0013] 3. The analysis and/or sorting system of any of the preceding embodiments, wherein the first separation region and the mixing region are connected by a first line; and/or the second separation region and the mixing region are connected by a second line.

[0014] 4. The analysis and/or sorting system of any of the preceding embodiments, further comprising at least one probe that contacts a sample comprising the target biological material. [0015] 5. The analysis and/or sorting system of any of the preceding embodiments, wherein the first mixture and the second mixture are received by separate inlets of the at least one second inlets.

[0016] 6. The analysis and/or sorting system of any of the preceding embodiments, wherein the analysis and/or sorting device comprises a flow cytometer.

[0017] 7. The analysis and/or sorting system of any of the preceding embodiments, wherein the analysis and/or sorting device sorts the target biological materials and/or particles based upon one or more of fluorescence, mass, buoyancy, and/or magnetism.

[0018] 8. The analysis and/or sorting system of any of the preceding embodiments, wherein the cleaving entity is selected from the group consisting of an endonuclease, a protease, and a g!ycosidase.

[0019] 9. The analysis and/or sorting system of any of the preceding embodiments, wherein the linker is selected from the group consisting of a nucleotide linker, a peptide linker, and a carbohydrate linker.

[0020] 10. The analysis and/or sorting system of any of the preceding embodiments, wherein the second mixture further comprises a second capture complex, which comprises a third separation entity linked via a third linker to a second binding entity, wherein the first binding entity binds to a first marker of the target biological material, and wherein the second binding entity binds to a second marker of the target biological material which is different from the first marker.

[0021] 11. A method, comprising: combining a first mixture and a second mixture, the first mixture comprising a first capture complex which comprises a first separation entity linked via a first linker to a first binding entity bound to a target biological material, and the second mixture comprising a cleaving entity linked via a second linker to a second separation entity, wherein the cleaving entity cleaves the first linker of the first capture complex; and collecting at least one first fraction enriched for the target biological material and at least one second fraction that is substantially devoid of the target biological material.

[0022] 12. The method of embodiment 11, further comprising, before contact between the first mixture and the second mixture, mixing the target biological material with a binding entity that binds to a marker of the target biological material. [0023] 13. The method of embodiment 12, wherein at least one of the separation entity, binding entity, and/or target biological material contains a label, wherein the label is selected from the group consisting of a fluorescent label, a magnetic label, an isotopic label, or a chemical label . [0024] 14. The method of either of embodiments 12 or 13, further comprising, in a first separation region, and after mixing the target biological material with the binding entity, separating the first separation entity complexed with the binding entity, the linker, and the target biological material from at least one selected from the group consisting of unbound binding entity, unbound linker, and unbound biological material.

[0025] 15. The method of embodiment 14, wherein the first separation entity is magnetic and the first separation region comprises an electromagnet, or magnet that attracts or repels the first separation entity.

[0026] 16. The method of any of embodiments 11-15, wherein the cleaving entity is selected from the group consisting of an endonuclease, a protease, and a glycosidase.

[0027] 17. The method of any of embodiments 11 - 16, wherein the linker i s sel ected from the group consisting of a nucleotide linker, a peptide linker, and a carbohydrate linker.

[0028] 18. The method of embodiment 14, wherein a second separation region separates cleaved target biological material from the first separation entity and the second separation entity.

[0029] 19. The method of embodiment 12, wherein the binding entity is an antibody, and wherein the marker is a surface antigen.

[0030] 20. A method, comprising: combining a first mixture and a second mixture, the first mixture comprising a first capture complex which comprises a first separation entity linked via a first linker to a first binding entity bound to a target biological material, and the second mixture comprising a cleaving entity linked via a second linker to a second separation entity, wherein the cleaving entity cleaves the first linker of the first capture complex; collecting at least one first fraction enriched for the target biological material and at least one second fraction that is substantially devoid of the target biological material: and administering the target biological material to a patient.

[0031] Additional features, advantages, and embodiments of the disclosed subject matter may be set forth or apparent from consideration of the following detailed description, drawings, and claims. Moreover, it is to be understood that both the foregoing summary and the following detailed description are exemplary and are intended to provide further explanation without limiting the scope of the claims.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS [0032] The accompanying drawings, which are included to provide a further understanding of the disclosed subject matter, are incorporated in and constitute a part of this specification. The drawings also illustrate embodiments of the disclosed subject matter and, together with the detailed description, explain the principles of embodiments of the disclosed subject matter. No attempt is made to show structural details in more detail than may be necessary for a fundamental understanding of the disclosed subject matter and the various ways in which it may be practiced.

[0033] Fig, 1A shows a cross-sectional view of an example of an analysis and sorting system including an analysis and sorting device according to an implementation herein.

[0034] Fig. IB illustrates an example in which an analysis and sorting device is a FACS-enabled flow cytometer.

[0035] Fig. 2A show_'s an example of a probe oriented to collect a sample from a well in well plate.

[0036] Fig. 2B shows an example of a probe collecting a sample from a w'ell in well plate.

[0037] Fig. 3 A shows an example of a cross-sectional view of an example of a probe having an open end.

[0038] Fig. 3B shows an example of a perspective view of an example of a probe having an open end. [0039] Fig. 4 shows an example of a probe in which conduits of the fluid supply and/or the fluid exhaust may be provided in a parallel direction.

[0040] Fig. 5A shows a first example of a configuration for the mixing region.

[0041] Fig. 5B shows a second example of a configuration for the mixing region.

[0042] Fig. 5C shows a third example of a configuration for the mixing region.

[0043] Fig. 6 shows an example of a capture complex and cleaving complex according to an implementation disclosed herein.

[0044] Fig. 7 A shows a set of initial components in a mixture including a first capture complex to be used in an example of an analysis and sorting system in which multiple separations are performed in series.

[0045] Fig. 7B show_'s a first cleaving complex and a second capture complex to be added into a mixture in an example of an analysis and sorting system in which multiple separations are performed in series.

[0046] Fig. 7C shows contents of a mixture after the first cleaving complex and second capture complex are added and mixed, in an example of an analysis and sorting system in which multiple separations are performed in series.

[0047] Fig. 7D shows a further second cleaving complex for use in an example of an analysis and sorting system in which multiple separations are performed in series.

[0048] Fig. 7E shows contents of a mixture after the second cleaving complex is added and mixed, in an example of an analysis and sorting system in w'hich multiple separations are performed in series. [0049] Fig. 8 shows an example method of separating, enriching for, and/or analyzing target biological materials.

DETAILED DESCRIPTION OF THE INVENTION [0050] The following discussion is directed to various exemplary implementations. However, one possessing ordinary skill in the art will understand that the implementations disclosed herein have broad application, and that the discussion of any implementation is meant only to be an example of that implementation, and not intended to suggest that the scope of the disclosure, including the claims, is limited to that implementation.

[0051] Fig. 1 A shows an example of an analysis and sorting system according to an implementation herein. Analysis and sorting system 10 may be provided in the presence of well plate 50. In this example, analysis and sorting system 10 may include probe 11, first separation region 71, mixing region 76, second separation region 78, and analysis and sorting device 23. Probe input line 31a may be configured to provide a fluid to probe 11. Probe output line 31b may be configured to remove or receive a sample and/or fluid from probe 11 and/or provide sample and/or fluid from probe 11 to first separation region 71 or first separation region pump 42. Probe to first separation region line 70 may be configured to provide sample and/or fluid from probe 11 to first separation region 71. First separation region to mixing region line 73 may be configured to provide sample and/or fluid from first separation region 71 to mixing region 76. Mixing region to second separation region line 77 may be configured to provide sample and/or fluid from mixing region 76 to second separation region 78. Second separation region to analysis and sorting device line 32 may be configured to provide sample and/or fluid from second separation region 78 to analysis and sorting device 23. A “region” can refer to an enclosed area of analysis and sorting system 10 capable of having fluid present within it and/or flowing through it to perform an attributed function, such as one or more sections of tubing, channels, cartridges, chambers, or reservoirs. Fig. 1A illustrates an example of a region as a chamber, which has a larger volume than the tubing connected thereto. Analysis and sorting device 23 can be, for example, a flow cytometer 20 or a fluorescence-activated cell sorting (FACS) device. Other sorting devices that utilize magnetism, such as a MACS device or a MICS device such as the one described by Mair et ah, can be used as the analysis and sorting device. Fig. IB illustrates an example in which analysis and sorting device 23 is a FACS-enabled flow cytometer 20. A “flow cytometer” can be any device suitable for detection of a property or properties of a collection of biological materials in a fluid suspension, and measurement and/or sorting based on the property or properties, using the fluidity of the suspension. A flow cytometer 20 may detect a property or properties which are indicated by or associated with a label, such as a fluorescent, magnetic, isotopic, or chemical label. Such a iabel may be a property of a separation entity itself or binding entity itself, or provided within the separation entity or binding entity and/or on a surface of the separation entity or binding entity, either directly or via a linking group. Additionally or alternatively, a flow cytometer 20 may detect a property or properties unrelated to any label, for example wherein the property is the size, shape, density, binding capability, conductivity, or acoustic properties of a biological material, A flow cytometer 20 may isolate a target fraction of biological materials, or also be capable of isolating single or individual target biological materials. “Biological material” can refer to any particulate or molecular component of a sample to be analyzed and/or sorted, including, but not limited to, one or more cells, cell fragments, viruses, virus fragments, organelles, exosomes or extracellular vesicles and fragments thereof, proteins, nucleic acids, and/or carbohydrates. “Target” biological material can refer to any biological material having one or more markers and/or possessing one or more properties, which is intended to be recognized by a binding entity and/or its affiliated separation entity and/or label.

[0052] In some embodiments, for example as shown in Fig. 1 A, analysis and sorting system 10 can include an autosampler 43. In some embodiments, autosampler 43 may include a holder for control] ably holding and releasing probe 11, and for moving probe 11 between multiple sample containers and wells. In other embodiments, autosampler 43 may be fixedly attached or integral with probe 11, and may be configured to move probe 11 between multiple sample containers and/or wells. In still other embodiments, probe 11 may be configured to maintain a substantially fixed position during operation, while autosampler 43 includes a holder for controllably holding and releasing a sample container, such as a sample holder, tube, and/or well plate, and for moving such a sample container to provide multiple samples for sampling by probe 11 in its fixed position. [0053] Autosampler 43 may be configured to move probe 11 between wells 51a, 51b, and 51c of well plate 50. Well plate 50 may have any number of wells 51a, 51b, and 51c, including 1, 6, 12, 24, 48, 96, 384, or 1536 wells, and such wells may be provided in a well plate format. In some configurations, autosampler 43 and/or probe 11 may accommodate sampling from samples in larger volume containers or tubes, such as tubes containing patient blood samples or cultured cells. Examples of larger volume containers include 1.5 mL microcentrifuge tubes; from 5 to 250 rnL tubes; from 50 to 500 ml, bottles; and/or vacutainer tubes. Other examples of large volume containers include T25, T75, and T150 cell culture flasks.

[0054] In Fig. 1A, the embodiment of probe 11 is depicted in an orientation such that an open end thereof would be pointing downward during operation. However, in other embodiments, for example where the wells or other sample container or containers are sufficiently narrow so as to retain the sample by forces such as surface tension or adhesion even in other orientations, the open end of probe 11 may point in an upward direction, a sideways direction, or at a skew angle with respect to a vertical direction. In some such embodiments, an upward direction for probe 11 and an inverted orientation of the sample container or containers, wherein an open end of the sample container or containers faces downward, may be particularly preferred.

[0055] In some embodiments, analysis and sorting system 10 may orient probe 11 such that it can be directed into a sample container, such as a sample holder, tube, cartridge, microchip, and/or well plate 50, or compartments within a compartmentalized container or array or collection of containers. Probe 11 may be a syringe or a pipette. Probe 11 may utilize positive displacement, air displacement, peristaltic, or other dispensing technology to aspirate, dispense, draw, remove, etc. fluid. Probe 11 may be sheathed in disposable and/or washable tips. Fig. 2A shows an example of probe 11 oriented to collect a sample from well 51 in well plate 50. Fig. 2B shows an example of probe 11 collecting a sample from well 51 in well plate 50. In the embodiments shown in Figs. 1 A, IB, 2A, and 2B, autosampler 43 may reposition probe 11 for collection of samples in wells 51a, 51b, and 51c in well plate 50. In other embodiments, autosampler 43 may he configured to reposition well plate 50 for collection of samples in wells 51a, 51b, and 51c by probe 11, and probe 11 may be provided in a stationary position. [0056] Autosampler 43 may be configured to collect separate samples and/or fluid from different wells or other containers at a rate of greater than 30 per minute, preferably at least 35 per minute, preferably at least 40 per minute, more preferably at least 45 per minute, even more preferably at least 60 per minute, and still further preferably at approximately 96 per minute. In some embodiments, autosampler 43 may be configured to collect separate samples and/or fluid from different wells or other containers at a rate of as high as 110 per minute or less. Embodiments involving these sample collection rates may particularly be embodiments in which probe 11 is configured for at least partial insertion into one or more sample containers, preferably a well 51 or wells in a well plate 50 or one or more such well plates. In cases where multiple probes 11 are utilized in parallel, the sampling rate may be multiplied accordingly, such as if autosampler 43 is configured to hold and/or move four probes simultaneously to collect samples and/or fluid from four different wells in parallel. In another embodiment, autosampler 43 may be configured to hold and/or move 2, 4, 6, 8, 16, 20, 24, 30, 48, 96, or more probes 11 in parallel.

[0057] Fig. 3 A shows an example of a cross-sectional view of an example of probe 11 having an open end. Fig. 3B shows a perspective view of the same or similar embodiment. Fig. 4 shows such an embodiment in use. In such embodiments, probe 11 may include an outer wall 103, an open end 102 at an end of the outer wail 103 which in these views is pointed upward, a fluid supply 104 configured for providing fluid to the open end 102, and a fluid exhaust 105 configured for removing fluid from open end 102.

[0058] Fluid supply 104 may be an annular region immediately within outer wall 103, and fluid exhaust 105 may be a coaxial conduit positioned centrally in probe 11, In some embodiments, an opening of fluid exhaust 105 may not extend axially for the entire length of outer wall 103 extending to open end 102, leaving some space at open end 102 for flow to more readily occur.

In other embodiments, an opening of fluid exhaust 105 may extend axially for the entire length of outer wall 103 extending to open end 102, or may extend axially even further than the entire length of outer wall 103 and out from open end 102.

[0059] In other embodiments, fluid supply 104 and fluid exhaust 105 can be configured differently. For example, fluid exhaust 105 may be an annular region immediately within outer wall 103, and fluid supply 104 may be a coaxial conduit positioned centrally in probe 11. In some embodiments, fluid supply 104 may be provided as one or more fluid supply conduits and/or fluid exhaust 105 may be provided as one or more fluid exhaust conduits. Conduits of fluid supply 104 and/or fluid exhaust 105 may be provided in a parallel direction as shown in Figs. 3A, 3B, and 4 and/or at oblique angles from one another.

[0060] In the embodiment shown in Fig. 4, probe 11 may provide flow of a fluid along a flow path 106. Fluid supply 104 can provide a fluid to open end 102 of probe 11 along incoming flow path 106a, then the fluid can flow through open end 102 along open-end flow path 106b, then the fluid can flow into outgoing flow path 106c through fluid exhaust 105. In this or other embodiments, open-end flow_' path 106b can include paths of flow which are less direct, extending into open end 102 which then forms fluid dome 107. To measure or control the flow of a fluid inward through fluid supply 104, fluid supply 104 can include a flow meter and/or a flow regulator. Similarly, but independently, to measure or control the flow' of a fluid outward through fluid exhaust 105, fluid exhaust 105 can include a flow meter and/or a flow regulator, and/or may include a sensor, for example a light-based sensor, which can monitor the size, curvature, and/or other parameters of dome 107 to provide data for maintaining optimal flow into or out of probe 11

[0061] The material or materials constituting probe 11 are not particularly limited. The configuration of the probe is not particularly limited. For example, the probe may be a syringe, pipette, or other type of sampling device. Any of outer wall 103, fluid supply 104, and/or fluid exhaust 105 can include at least one metal, metal alloy, plastic, glass, ceramic, or any combination thereof, preferably including stainless steel and/or medical-grade plastic. Any part or entirety of outer wall 103, fluid supply 104, and/or fluid exhaust 105 can be coated or uncoated, preferably coated with a hydrophobic or hydrophilic coating. In some embodiments, at least a portion of outer wall 103, fluid supply 104, and/or fluid exhaust 105 can include a hydrophilic material or he provided with a hydrophilic coating, thereby providing an adhesive effect with a fluid flowing along flow path 106 and/or the fluid in fluid dome 107. In the same or other embodiments, at least a portion of outer wall 103, fluid supply 104, and/or fluid exhaust 105 can include a hydrophobic material or be provided with a hydrophobic coating, thereby avoiding an adhesive effect with a fluid in order to better form a desired dome shape for fluid dome 107.

[00621 In some embodiments, probe 11 can further include a fluid collection conduit, configured to collect excess or overflowing fluid from open end 102, Such a fluid collection conduit may be positioned within or provided on outer wall 103. The fluid collection conduit can include one or more openings, preferably located proximaliy to open end 102. The one or more openings of the fluid collection conduit can be one or more annular openings or multiple openings in an annular arrangement.

[0063] In some embodiments as shown in Figs. 2A and 2B, probe 11 may be configured for at least partial insertion into one or more sample containers, preferably a well 51 or wells in a well plate 50 or well plates. In these embodiments, an outer width w of probe 11 is preferably less than an inner width w^! of well 51, thereby allowing for insertion of probe 11 into well 51. The outer width w of probe 11 may be the width of probe 11 at open end 102 or, more preferably, may be the width of probe 11 at an axial distance from open end 102 which is less than or approximately equal to the depth of well 51. In some embodiments, outer width w of probe 11 may be less than 7.0 mm, less than 5.0 mm, less than 3.3 mm, less than 1.7 mm, or less than 1.3 mm. In some embodiments, outer width w of probe 11 may be a width of the probe at the open end 102 of probe 11, or at an axial distance of from 5.0 to 25.0 mm from the open end 102 of probe 11, or at an axial distance of from 6.5 to 11.5 mm from the open end 102 of probe 11.

[0064] In other embodiments, probe 11 may not necessarily be configured for insertion into a sample container. For example, some embodiments of probe 11 and/or analysis and sorting system 10 may be suitable for use with an apparatus for transmitting a sample from individual wells within a well plate to the open end 102 of probe 11, such as with an automated pipetting system, or by directing acoustic energy into the samples within individual wells to eject droplets of the sample. In these embodiments, the open end of the probe may point in an up ward direction, downward direction, sideways direction, or at a skew angle with respect to a vertical direction. In some such embodiments, an upward direction for the probe and an inverted orientation of the sample container or containers may be particularly preferred. In still other embodiments, probe 11 may be configured to receive one or more samples without direct sampling from wells in a well plate, for example in the provision of drops or other small quantities of one or more samples directly to the open end 102 of probe 11.

[0065] In some embodiments, analysis and sorting system 10 has only one probe 11 and no more. In other embodiments, analysis and sorting system 10 can include one or more probes. Probe 11 may refer to an assembly having multiple probes 11 attached thereto such that fluid from multiple wells 51a, 51b, and 51c of rvell plate 50 can be simultaneously processed. Probes 11 may refer to 1, 2, 3, 4, 8, 16, 24, 48, 96, 384, or 1536 probes 11 acting simultaneously to intake and/or exhaust fluid and/or sample from wells 51a, 51b, and 51c of well plate 50.

[0066] In certain embodiments, analysis and sorting device 23 is a flow' cytometer 20 and can include a flow cell 21, a laser 22, and at least two containers 61a and 61b, which can be, for example, wells in multiple well plates or wells in the same well plate, as shown in Fig. IB. Flow- cytometer 20 is not particularly limited, except in that it is configured to analyze and sort components of a fluid stream from probe 11 that are received via the second separation region to analysis and sorting device line 32. In particular, flow cytometer 20 may be configured to sort a sample into at least two containers 61a and 61b, such as a positive fraction and negative fraction. A positive fraction may contain or be enriched for, as described below, desirable biological materials and a negative fraction may not contain or be depleted of, as described below, desirable biological materials. For instance, in some embodiments, it may be of interest to sort and enrich desirable target biological materials into a positive fraction, while the remaining undesirable sample or fluid flow, depleted of desirable target biological materials, is sorted into a separate negative fraction. In other embodiments, it may be of interest to remove or deplete undesirable target biological materials from a desirable sample or fluid flow. In such other embodiments, separation by analysis and sotting system 10 may serve the purpose of removing or depleting undesirable target biological materials into a separate negative fraction from a desirable sample or fluid flow, after which the remaining desirable sample or fluid flow is to be collected into a positive fraction for further analysis. [0067] In some configurations, another container 61c may receive discarded fluid such as fluid from a wash step. A fluid stream provided to flow cytometer 20 can pass into flow cell 21, which can regulate the fluid stream such that many or most biological materials or other components of the sample in the fluid stream emerge individually in separate droplets. In some embodiments, flow cell 21 can regulate a fluid stream and its components provided to flow cytometer 20 by using ultrasonic waves to acoustically focus biological materials and other components of the stream, enhancing throughput and preventing clogging. In some embodiments, flow cell 21 can regulate a fluid stream and its components provided to flow cytometer 20 by filtering and/or preventing the flow through of aggregated biological material or components greater than the desired size of the target biological material. In certain embodiments, the fluid stream thus regulated then passes through a measuring system. The measuring system can be, but is not limited to, an impedance, conductive, size exclusion, filtration, acoustic, thermodynamic, electromagnetic, mass spectrometric, or optical system. In some embodiments, the measuring system can include a laser beam emitted from laser 22, which can excite one or more fluorescent labels in a sample in the fluid stream. A detector can then detect the presence or absence of the one or more fluorescent labels by the presence or absence of fluorescence. Some embodiments include more than one laser and/or more than one detector. In certain embodiments, droplets are charged, and droplets containing biological materials labeled with the one or more fluorescent labels are sorted by their charges into one container 61a, while droplets containing biological materials not labeled with the fluorescent label or labels are sorted into a different container 61b, as shown in the embodiment in Fig. IB. In other embodiments, droplet-based sorting is not used and instead, labeled target biological materials are sorted out of a fluid flow into one container 61a using a magnetic solenoid sorting valve, while unlabeled biological materials are sorted into a different container 61b. As further shown in Fig. IB, these containers can be separate wells of a well plate, for example a microplate. In some configurations, flow cytometer 20 may sort samples into larger volume containers, tubes, cartridges, or microchips such as described above.

[0068] In other embodiments, flow' cytometer 20 may be configured for analysis of the sample and collection of data about the presence, content, frequency, and/or distribution of components within the sample having different properties, or satisfying various parameters. In particular, the flow' cytometer 20 may be configured to measure and collect data as to the presence and/or frequency of a labeled component, such as a labeled biological material, a labeled analysis reagent, or labeled particulate component. In some embodiments, flow cytometer 20 may be configured for both analysis and sorting, as both described above. In other embodiments, the flow cytometer 20 may be configured for analysis alone without sorting, and the fluid stream including the sample may be discarded after analysis. A fluid stream may include, for example, biological materials, including both desirable biological materials and undesirable biological materials, separation entities, binding entities, labels, and a fluid. The fluid may include water and/or a buffer. Examples of buffers may include phosphate buffered saline (PBS), tris-chioride, 2,2-Bis(hydroxymethyl)-2,2',2"-nitrilotriethanol (Bis-Tris), 4-(2 -hydroxy ethyl)- 1 - piperazineethanesulfonic acid (HEPES), Sodium acetate trihydrate, N-(2-Hydroxy-l, 1 - bis(hydroxymethyl)ethyl)glycine (tricine), 1,4-Piperazinediethanesulfonic acid, Piperazine- 1, 4- bi s(2~ethanesulfonic acid), Piperazine~N,N'~bis(2-ethanesulfonic acid) (PIPES), citric acid buffers, sodium acetate buffers, sodium carbonate buffers . Generally, a buffer can be selected based upon the properties of the target biological material including, but not limited to, pH, pKa, salt concentration, temperature, stability, etc. Other components may be added to the fluid at any point in the analysis and sorting system 10.

[0069] In still other embodiments, analysis and sorting device 23 is a microfluidic analysis and sorting device configured for the sorting of samples into at least two containers 61a and 61b or other receiving points as directed by the microfluidic analysis and sorting device, for example, wells in multiple well plates or wells in the same well plate, as shown in Fig, IB, or large volume containers. One container may contain samples containing target biological materials, while another container may receive untargeted biological materials that are undesirable. Microfluidic analysis and sorting device 23 is not particularly limited, except in that it is configured to sort components of a fluid stream from probe 11 based on any fluorescent, magnetic, isotopic, or chemical label or labels provided on the components, and/or based on a property or properties of the components unrelated to any label such as size, shape, density, binding capability, conductivity, or acoustic properties. For example, microfluidic analysis and sorting device 23 can be a MACS or a MICS device. A fluid stream provided to the microfluidic analysis and sorting device can be regulated by the microfluidic analysis and sorting device such that many or most biological materials of the sample in the fluid stream are separated into distinct components based on the labels and/or properties mentioned above. In certain embodiments, components containing a given set of labels and/or properties are separated and sorted into one container 61a, while components lacking the given set of labels and/or properties are sorted into a different container 61b, as shown in the embodiment in Fig. IB. These containers can be separate wells of a well plate, for example a microplate, and/or a large volume container as described earlier. In some embodiments, for example in embodiments that do not involve analysis or sorting based on fluorescence or any other light- or radiation-based phenomenon, a microfluidic analysis and sorting device 23 may not include a laser, in contrast with the embodiment of Fig. IB, showing laser 22.

[0070] In some embodiments, for example as shown in Figs. 1 A and IB, analysis and sorting system 10 can include a probe input line 31a, configured to supply a fluid to probe 11, and a probe output line 31b, configured to convey fluid from probe 11. Probe input line 31a is not particularly limited beyond its configuration for conveying a fluid stream to probe 11, Probe input line 31a can be joined to or integral with fluid supply 104 to provide fluid to fluid supply 104 shown in Figs. 3 A, 3B, and 4. Probe output line 31b is not particularly limited beyond its configuration for conveying a fluid stream from probe 11 to first separation region 71. Probe output line 31b can be joined to or integral with fluid exhaust 105 to convey fluid from fluid exhaust 105 shown in Figs. 3A, 3B, and 4. Second separation region to analysis and sorting device line 32 is not particularly limited beyond its configuration for conveying fluid from probe 11 to analysis and sorting device 23, Probe to first separation region line 70 is not particularly limited beyond its configuration for conveying a fluid stream from probe 11 to first separation region 71. First separation region to mixing region line 73 is not particularly limited beyond its configuration for providing a fluid stream from first separation region 71 to mixing region 76. Mixing region to second separation region line 77 is not particularly limited beyond its configuration for providing a fluid stream from mixing region 76 to second separation region 78. Reagent reservoir to mixing region line 80 is not particularly limited beyond its configuration for providing a fluid from reagent reservoir 74 to mixing region 76.

[0071] Line 31a, 31b, 32, 70, 73, 77, 80 can be rigid, partially rigid, or flexible. Line 31a, 31b, 32, 70, 73, 77, 80 is preferably a closed and sealed line to prevent the introduction of air or gas into the fluid which it conveys. It can include a tube, hose, pipe, conduit through another element, or any combination thereof. It can be made of metal, glass, plastic, rubber, or any combination thereof, or any other material or combination of materials which can convey fluid to and from probe 11. Preferably, line 31a, 31b, 32, 70, 73, 77, 80 includes silicone or PVC tubing. In some embodiments, line 31a, 31b, 32, 70, 73, 77, 80 can include or exclude valves, joints, and/or junctions. Preferably, line 31a, 31b, 32, 70, 73, 77, 80 excludes any reciprocating valve.

In some embodiments, line 31a, 31b, 32, 70, 73, 77, 80 can include or exclude sample loops, preferably excluding sample loops. The material or materials of one line 31a, 31b, 32, 70, 73, 77, 80 may differ from the material or materials of another line.

[0072] In some embodiments, for example as shown in Figs. 1 A and IB, line 31a, 31b, 32, 70, 73, 77, 80 can include or be interrupted by one or more pumps. Probe input pump 41 may be configured to supply a fluid to probe 11. Probe input pump 41 may be configured to move, convey, or propel a fluid through probe input line 31a to probe 11, and first separation region pump 42 may be configured to move, convey, or propel a fluid through probe 11 to first separation region 71, away from probe 11 and/or into first separation region 71. Reagent reservoir pump 75 may be configured to move, convey, or propel a fluid from reagent reservoir 74 to mixing region 76. Pump 41, 42, 75 may be positioned differently from those shown in Figs. 1A and IB and/or omitted from analysis and sorting system 10 to the extent that one or more pumps are not required to convey or draw fluid/sample through analysis and sorting system 10. For example, a pump may be disposed between first separation region 71 and mixing region 76, between mixing region 76 and second separation region 78, and/or between second separation region 78 and analysis and sorting device 23. Reagent reservoir pump 75 may be disposed between reagent reservoir 74 and mixing region 76. Pump 41, 42, 75 can be any of various types of laboratory pumps including peristaltic pumps, diaphragm pumps, syringe pumps, gear pumps, or microfluidic pumps. Preferably, pump 41, 42, 75 is a microfluidic pump. In configurations where multiple pumps 41, 42, 75 are used, the pumps may be the same type or a different type from one another.

[0073] In some implementations, a fluid can be conveyed through line 31a, 31b, 32, 70, 73, 77, 80 in other ways. For example, a vacuum in or near probe 11 can reduce pressure at or near the end of probe input line 31a, thereby causing the pressure (for example, ambient pressure) at a source of the fluid to push the fluid through probe input line 31a. Force can also be applied to the fluid to convey it through probe input line 31a. for example, by siphoning, or by gravity, from an elevated fluid source. The skilled artisan will understand that other methods of conveying fluid through line 31a, 31b, 32, 70, 73, 77, 80 are known and may be suitable for conveying the fluid through analysis and sorting system 10.

[0074] In some embodiments, for example as shown in Figs. 1A and IB, analy sis and sorting system 10 can further include a control system for controlling fluid from probe input pump 41 and probe 11 to first separation region pump 42. The control system can monitor the flow of fluid through line 31a, 31b, 32, 70, 73, 77, 80 and/or pump 41, 42, 75. The control system can optionally include one or more flow meters for monitoring fluid flow through one or more lines 31a, 31b, 32, 70, 73, 77, 80 and/or through one or more pumps 41, 42, 75. The control system can adjust the pumping power or other determinative parameters for pump 41, 42, 75. The control system can include a graphical user interface. The control system can be integrated with or separate from a control system for analysis and sorting device 23.

[0075] First separation region 71 can have one or more inlets 91a corresponding to where a line or lines connects to first separation region 71 to provide sample and/or fluid. In some eases, two or more lines may be joined by a Y connection resulting in one inlet 91a into first separation region 71. In some configurations, each line may separately connect to first separation region 71 so that multiple inlets 91a to first separation region 71 are formed. First separation region 71 as illustrated in Figs. 1A and IB has one inlet 91a corresponding to probe to first separation region line 70. Multiple inlets may be formed, for example, where the same material is being separated and can be combined in first separation region 71. Inlets 91a may he provided for input of sample, labels, separation entities, cleaving entities, buffer, wash fluid, etc. In some configurations, multiple first separation regions 71 may be disposed in parallel and/or in a series in analysis and sorting system 10.

[0076] First separation region 71 can have one or more outlets 93a corresponding to where a line or lines 73 connects first separation region 71 to mixing region 76 to provide sample and/or fluid to mixing region 76. in some cases, a line may be split, for example, by a Y connection resulting in multiple lines from a single outlet 93a. Each line may connect to a separate mixing region 76, for example, where it is desired to mix combinations of sample, labels, separation entities, cleaving entities, buffer, wash fluid, etc. in parallel. First separation region 71 as illustrated in Figs. 1A and IB has one outlet corresponding to first separation region to mixing region line 73.

[0077] First separation region 71 may utilize any of one or more different mechanisms to separate, impede the flow of, sequester, or remove target, biological materials from the fluid stream. Different mechanisms may include, for example, sedimentation (e.g, using gravitational force or centrifugal force), buoyancy, and/or magnetic separation.

[0078] Figs. 1A and IB illustrate an example where first separation region 71 utilizes one or more magnets 72a, 72b, which in some configurations may be electromagnets. Fluid provided from probe 11 may include sample. Sample may include a solution (e.g, buffer and/or water) such as one or more that make up the fluid as described earlier as well as biological materials and/or separation entities such as beads. In some configurations, target biological materials are magnetically labeled, which may cause the biological materials to respond to a magnetic field or magnetic field gradient. A magnet 72a, 72b may be removable or integral with first separation region 71. For example, magnet 72a, 72b may correspond to a magnet that can rest on the region or otherwise be fastened to the region. In some configurations, a magnet can be moved along and/or away from the region to control the location and strength of the magnetic field in the region. In other configurations, magnet 72a, 72b is an electromagnet. The electromagnet may be manually and/or mechanically operated or controlled by a computer, for example as a part of an automated system. For example, analysis and sorting system 10 may be computer controlled. As a part of the automated process, the strength and/or duration of the magnetic field may be controlled. The electromagnet composition and/or structure is not particularly limited. The electromagnet may be made of any suitable material such as a magnetic core of iron, cobalt, nickel, and/or steel. The composition of the electromagnet may be configured to a desired application. Some materials may produce a stronger magnetic field. In the presence of a magnetic field in first separation region 71, magnetically labeled biological materials may be sequestered in first separation region 71. Other methods of separation may be readily adapted in lieu of or in addition to magnetic separation, for example separating target biological materials labeled with buoyant separation entities such as beads. In such configurations, magnet 72a, 72b may not be present.

[0079] The target biological materials may be labeled directly or indirectly with a fluorescent, magnetic, buoyant, or sedimentary' separation entity. A “separation entity” may refer to a particle such as a bead, microbead, nanobead, microparticle, nanoparticle, microsphere, or nanosphere, or a functionalized surface within a region of the system, with functional properties that enable its separation, isolation, or purification, or the separation, isolation, or purification of species it is directly or indirectly linked or bound to, from a heterogenous mixture. Examples of such functional properties can include a label, linkage to a binding entity recognizing a target biological material, chemical composition (e.g, a coating), charge, or hydrophobicity. Such a label may be a property of the separation entity or provided within the separation entity and/or on a surface of the separation entity, either directly or via a linking group. In some confi gurations, the separation entity may have more than one fluorescent, magnetic, buoyant, and/or sedimentary' property. For example, the separation entity_' may be fluorescently and magnetically labeled. Both of these properties may be used simultaneously or in a series in analysis and sorting system 10 to separate target biological materials from background biological materials or undesired components. In some embodiments, target biological materials may first be simultaneously labeled with both separation entities compatible with the separating mechanisms of the separation regions, as well as additional reagents for analysis and sorting by analysis and sorting device 23. For example, when the analysis and sorting device is a flow cytometer 20 and the separating mechanism of the separation regions is magnetic, target biological materials may initially be simultaneously labeled with both magnetic separation entities for separation in the separation regions, as well as fluorescently labeled reagents, such as fluorescently labeled binding entities and/or fluorescent dyes, for analysis and sorting in flow cytometer 20.

[0080] In some configurations, the population of separation entities may contain separation entities recognizing different properties and/or binding to different markers of multiple different target biological materials, either directly or indirectly through different binding entities, while having the same or different types of labels. For example, in a sample containing multiple different types of target biological materials with different properties, a population of separation entities with the same type of label but recognizing different properties and/or binding to different markers of the multiple different target biological materials may be used to separate and/or release multiple different target biological materials at the same time. In a similar example, but using separation entities that also have different types of labels, the population of separation entities may also separate and/or release multiple different target biological materials in one or more of the different separation regi ons according to the separation mechanism s of each separation region.

[0081] Capture complex separation entity 670 may be crosslinked or otherwise linked to a capture complex linker 660 which may link to a capture complex binding entity 650 as shown in Fig. 6, A “binding entity” may be an antibody, lectin, protein or polypeptide, nucleic acid, aptamer, or any molecule that recognizes or otherwise binds to a marker on a target biological material. A “marker' can be any molecule, such as a protein, lipid, carbohydrate, nucleic acid, chemical species, or biological species, that can be recognized and bound to by a binding entity. For example, an antibody may recognize a surface antigen of a target biological material or recognize a protein of interest, or a nucleic acid sequence may have strong affinity for a biological material of interest such as a protein. Similarly, a ligand may be presented as a binding entity that, has a strong affinity for a protein in the sample, or a protein may be presented as a. binding entity that has a strong affinity for a ligand in the sample. A “linker” may be a protein or polypeptide, carbohydrate or polysaccharide, nucleic acid, chemical, or other structural moiety that connects two species. Capture complex linker 660 may be a linker that connects capture complex binding entity 650 to capture complex separation entity 670. In some instances, capture complex linker 660 may be a part of capture complex binding entity 650 (e.g, be integrated with the binding entity). For example, a protein being used as capture complex binding entity 650 may be modified to include, for example, a. conjugatable feature that links it to capture complex separation entity 670, or a digestible or cleavable protein sequence at the N- or C-terminus. Capture complex linker 660 may, therefore, have a. capture complex cleavage site 665 that can be digested, cut, released, or otherwise controlled to release the target biological material 661 from capture complex separation entity 670. A capture complex 601 may therefore be formed between capture complex separation entity 670, capture complex linker 660, capture complex cleavage site 665, capture complex binding entity 650, and target biological material 661.

[0082] Returning to the magnetic separation example, some magnetic separation entities may form a complex with a binding entity such as an antibody, and still further some of the magnetic separation entities may form a complex with the antibody which binds to and labels a target biological material. Each of these species may be sequestered or have their flow impeded in first separation region 71 of Figs. 1 A and IB in the presence of a magnetic field. Similarly, separation entities used in other separation mechanisms such as buoyancy beads may sequester, impede, and/or divert the flow of these target biological materials in first separation region 71 in a manner that separates them from the nontarget, unbound sample, and/or fluid components of the fluid stream. Unbound biological materials as well as other non targeted components of the fluid stream, or unincorporated reagents such as unbound binding entity or binding entity not bound to a separation entity, may flow' through the remainder of analysis and sorting system 10 as a part of the fluid stream. Unbound fractions may be separated from the bound, labeled target biological materials, therefore, by application of the separation mechanism (e.g., a magnetic field), followed by flowing fluid to wash or flow unbound fractions from first separation region 71 onward through the remainder of analysis and sorting system 10. Because unbound fractions may flow through and/or be removed from analysis and sorting system 10 at first separation region 71, at least 90, 91, 93, 95, 96, 97, 98, 99, 99.5, 99.8%, or more of target biological materials remaining in the region may be those bound to the binding entity and linked to a separation entity. Bound, labeled target biological materials can then be released by removing and/or reducing the presence of the separation mechanism (e.g., a magnetic field or electromagnet).

[0083] In some configurations where magnetic separation is employed, first separation region 71 may include one or more magnets 72a, 72b. In some configurations, magnets 72a, 72b may be presented in a variety of paterns. For example, Figs. 1A and IB illustrate magnets 72a, 72b at the relative top and bottom of first separation region 71. However, magnets 72a, 72b may correspond to columns that extend into the interior of first separation region 71. Such a configuration may be desirable to ensure the capture of magnetic separation entities and/or magnetically labeled biological materials, and/or to affect the flow rate of sample and/or fluid through at least first, separation region 71. The likelihood of capture by the magnetic field may be increased by increasing the duration of the sample and/or fluid in first separation region 71. The magnitude of the magnetic force exerted upon the magnetic separation entities and/or magnetically labeled biological materials, the flow rate, and/or the shape, dimensions, and/or structure of first separation region 71 may be configured to immobilize or impede the progress of labeled species through first separation region 71.

[0084] Magnets 72a, 72b may generate a magnetic field or a magnetic field gradient. In some configurations, one magnet 72a, 72b may have an opposite polarity of the other magnet 72a, 72b so that magnetic species can be repelled, moved, or pushed towards the other magnet 72a, 72b. For example, a magnetic field of one polarity generated by magnet 72b in first separation region 71 may be sufficient to drive magnetically labeled species towards the other magnet 72a of the opposite polarity. Both magnets may be located on the exterior and/or interior of first separation region 71, and/or be integral with first separation region 71. Magnetic forces that act upon each magnetic species may be related to magnetic separation entity size and/or geometry.

[0085] During washing processes, the structure and/or dimension of first separation region 71 may be constructed to make it more difficult to shear target biological materials bound to the labeling entity and/or remove or dislodge bound biological materials from the separation mechanism. Any number of wash steps may occur before, during, or after, the separation mechanism (e.g, a magnetic field) is activated or present. In some configurations, a washing process may occur constantly or in parallel with the separation mechanism due to a constant flow of provided buffer, media, or other fluid through analysis and sorting system 10, The wash steps may remove unbound biological materials (i.e., those not sequestered by the separation mechanism) such as those not having a magnetic label, unincorporated reagents such as binding entities not linked to a magnetic label, as well as biological materials in the sample that are not bound to a separation entity label either directly or via an intermediary such as a binding entity.

In the presence of the magnetic field, for example, magnetically labeled target, biological materials may be immobilized as a part of separating the target biological materials from other nontarget biological materials that are present in the sample and/or fluid provided to first separation region 71. [0086] First separation region 71 may be composed of any suitable material such as glass, thermoplastic, flexible tubing, silicon, elastomer, etc. It may be coated with any material and may be functionalized as is known in the art. First separation region 71 may also be functionalized by embedding or reinforcing its majority composition material with another material to impart certain separation properties to the region. For instance, in the case of magnetic separation, the region may be composed of a majority of an above material embedded with another material, such as particles or wires of the aforementioned metals, suitable to impart or strengthen magnetic properties to the region. In some configurations, the interior of first separation region 71 may be functionalized to act as the separation entity for target biological materials instead of other separation entities such as beads or particles. In such embodiments, a binding entity recognizing target biological materials may be linked to coat the interior of first separation region 71 through a cleavable linker. Target biological materials may then be separated or immobilized from the fluid flow' in the separation region when bound by the binding entity coating that recognizes the target biological materials. In such a configuration, target biological material may be released to proceed through analysis and sorting system 10 by providing a cleaving complex to first separation region 71 that recognizes the cleavable linker to release the binding entity and its bound target biological materials from the separation region into the fluid flow. Such a cleaving complex comprising a particle-based separation entity such as magnetic beads may be provided through probe 11 or a reagent reservoir connected through an inlet to first separation region 71, and separated from the final sample entering analysis and sorting device 23 by the separation mechanism employed by second separation region 78 corresponding to the separation entity, in this case magnetically,

[0087] The thickness of the material is also not particularly limited. Thickness of the material may affect, for example, penetration of a magnetic field into first separation region 71. The sample and/or fluid may flow generally from left to right through first separation region 71 as illustrated in Figs. 1 A and IB. in some configurations, the direction of flow may be reversed.

The rate and direction by which sample and/or fluid flows through the region may he controlled by one or more pumps. The biological materials and separation entities may experience gravity as a function of their mass and density. Thus, in the case of magnetic separation, the flow rate, the strength of the magnetic field, and composition and/or conformation of the magnetic and/or magnetically labeled biological materials and separation entities may be selected to ensure that the magnetic species are immobilized or impeded by magnets 72a, 72b. The flow rate may be selected to ensure that the biological materials and separation entities do not sediment or rest at the bottom of a line and/or first separation region 71 in some configurations, in the case of labeling target biological materials with buoyancy beads, however, it is desirable that the beads float towards the top of first separation region 71. The efficiency of separation may allow for the separation of single target biological materials based upon the label, biological material size/shape, separation entity size/shape, strength of the separation mechanism, flow rate, and size/structure of first separation region 71.

[0088] First separation region 71 is not particularly limited by its shape. The shape may affect the flow rate of sample and/or fluid. For example, a larger volume may decrease the flow through first separation region 71. In some configurations, the first separation region 71 corresponds to a position along a length of tubing in which a magnetic field is applied, and/or where the tubing is functionalized as described above. The shape of the tubing may be indistinguishable from tubing before and after the first separation region 71. First separation region 71 may accommodate any number of inlets 91a, outlets 93a, and/or magnets 72a, 72b or other structures suitable for different separation mechanisms. The location of inlets 91a, outlets 93a, and/or magnets 72a, 72b or other structures is not particularly limited. Magnets 72a, 72b may follow a contour or portion of a contour of first separation region 71, The shape and/or volume of first separation region 71 can affect the flow rate of sample and/or fluid through the separation region to an outlet. Volume can be inversely proportional to the flow rate. The effect of volume on flow rate can be further modified by including, for example, a pump to the system such as described in U.S. Pat. No. 10,240,186, the contents of which are incorporated herein by reference.

[0089] Mixing region 76 may be disposed between first separation region 71 and second separation region 78. The size, number, and shape of mixing region 76 may be configured for a desired flow rate, duration of sample and reagent mixing, and/or volume of fluid in mixing region 76. The direction of flow may be from left to right as illustrated in Figs. 1 A and IB. Sample and/or fluid from first separation region 71 may enter mixing region 76 from one or more inlets 91b and be expelled through one or more outlets 93b. Reagent and/or fluid from reagent reservoir 74 may enter mixing region 76 from one or more inlets 92b and be expelled through one or more outlets 93b. A reagent may include but is not limited to, for example, a capture complex, a cleaving complex, a cleaving entity, a separation entity, a binding entity, a label as described earlier, fluid as described earlier, water, etc. In some cases, two or more lines may be joined by a Y connection resulting in one inlet into mixing region 76. In some configurations, each line may separately connect to mixing region 76 so that multiple inlets 91b, 92b to mixing region 76 are formed. Similarly, a line may be split, for example, by a Y connection resulting in multiple lines from a single outlet 93b from mixing region 76. In some configurations, multiple first separation regions 71 and/or multiple reagent reservoirs 74 may have one or more inlets into the same mixing region 76. In some configurations, multiple mixing regions 76 may be operated in parallel. For example, where multiple samples are being processed simultaneously, analysis and sorting system 10 may include multiple instances of first separation region 71, reagent reservoir 74, mixing region 76, and/or second separation region 78, in parallel and/or in a series.

[0090] Figs. 5A, 5B, and 5C show examples of three different configurations for mixing region 76. The configuration of mixing region 76 is not particularly limited so long as the sample, reagent, and/or fluid inputs are mixed therein. In some configurations, the mixing that occurs in the mixing region is passive, whereby the structure or configuration of fluid channels can affect the amount of mixing. In some instances, the mixing may be active, whereby the mixing in mixing region 76 is carried mechanically, magnetically, electrically, and/or acoustically. Active mixing measures may be controllable by an end user or an automated system by using flow and pressure gradients, electrical voltages across the fluid, and/or mechanical elements such as a stirring bar.

[0091] In an embodiment as shown in Fig. 5 A, mixing region 76 may be configured to be a microfluidic mixing channel. In this configuration, the flow of sample and/or fluid from inlet 91b may intersect a flow of reagent from reagent reservoir 74 through line 80 and inlet 92b. Mixing may occur at the point of intersection 520 and/or throughout mixing region 76. Mixing region 76 shows the path 510 that reagent and/or sample and/or fluid flow through in the mixing region. The flow rate from inlets 91b, 92b may be adjusted to ensure suitable mixing of the reagent and/or sample and/or fluid.

[0092] In another embodiment as shown in Fig. 5B, mixing region 76 may be configured to be in a post array mixing configuration. In this configuration, multiple columns 530 may extend into the interior of mixing region 76 where the flow of sample and/or fluid from inlet 91b may intersect a flow of reagent from inlet 92b. Columns 530 may facilitate mixing of sample and/or fluid from inlet 91b as it enters and flows through mixing region 76 with reagent from inlet 92b. Columns 530 illustrated in Fig. 5B are square-shaped, but the structures are not. particularly limited in size and/or shape. For example, in some configurations, the columns may have a cylindrical shape or a blade-like shape, and/or may have profiles that include concave portions.

In some configurations, the structures may extend only partially into mixing region 76. In some configurations, the structures may not be disposed in a parallel or grid layout. For example, the structures may be tangled or curved.

[0093] In another embodiment as shown in Fig. 5C, mixing region 76 may employ mechanical mixing using a structure such as a stirring feature 540 and/or valve 550. In such a configuration, the valve may be user and/or computer controlled. Sample and/or fluid may enter mixing region 76 from inlet 91b and reagent may enter mixing region 76 from inlet 92b. During mixing, the valve may be closed so that no fluid exits mixing region 76. After sufficient mixing, the valve may be opened to convey fluid through mixing region 76. The size and shape of the mechanism that performs the mixing is not particularly limited. In the embodiment shown in Fig. 5C, it is a propeller. In some instances, for example, it may be a stirring bar. The speed of the mixing can be controlled, for example by a user and/or a computer.

[0094] Reagent reservoir 74 in Figs. 1A, IB, 5 A, 5B, and 5C may include a mixture of a cleaving complex 602 corresponding to a cleaving entity 610 linked directly or indirectly to a separation entity such as a cleaving complex separation entity 630 in Fig. 6. Cleaving complex 602 may be provided to mixing region 76 via one or more pumps 75 and/or lines 80 and/or inlets 92b. Mixing region 76 may homogenize or mix cleaving complex 602 received from the reagent reservoir with the mixture of sample and/or fluid received from first separation region 71, which may include, for example, labeled biological materials, binding entities such as antibody, and/or buffer or wash fluid.

[0095] Second separation region 78 can have one or more inlets 91c corresponding to where a line or lines connects to second separation region 78 to provide sample and/or fluid. In some cases, two or more lines may be joined by a Y connection resulting in one inlet 91c into second separation region 78. In some configurations, each line may separately connect to second separation region 78 so that multiple inlets 91c to second separation region 78 are formed.

Second separation region 78 as illustrated in Figs. 1 A and IB has one inlet 91c corresponding to mixing region to second separation region line 77. Multiple inlets may be formed, for example, where the same material is being separated and can be combined in second separation region 78, Inlets 91c may be provided for input of sample, labels, beads, buffer, wash fluid, etc. In some configurations, multipie second separation regions 78 may be disposed in parallel and/or in a series in analysis and sorting system 10.

[0096] Second separation region 78 can have one or more outlets 93c corresponding to rvhere a line or lines 32 connects second separation region 78 to analysis and sorting device 23 to provide sample and/or fluid to analysis and sorting device 23. In some cases, a line may be split, for example, by a Y connection resulting in multiple lines from a single outlet 93c. Each line may connect to a separate analysis and sorting device 23, for example, where it is desired to perform a separation in parallel. Second separation region 78 as illustrated in Figs. 1 A and IB has one outlet corresponding to second separation region to analysis and sorting device line 32.

[0097] Second separation region 78 may utilize any of one or more different mechanisms to separate, impede the flow of, sequester, or remove target, biological materials from the fluid stream. Different mechanisms may include, for example, sedimentation (e.g, using gravitational force or centrifugal force), buoyancy, and/or magnetic separation.

[0098] Figs. 1 A and IB illustrate an example where second separation region 78 utilizes one or more magnets 79a, 79b, which in some configurations may be electromagnets. Fluid provided from mixing region 76 may include sample. Sample may include a solution (e.g., buffer and/or water) such as one or more that make up the fluid as described earlier as well as biological materials, separation entities, and/or cleaving entities. In some configurations, target biological materials are magnetically labeled which may cause the biological material to respond to a magnetic field or magnetic field gradient, A magnet 79a, 79b may be removable or integral with second separation region 78. For example, magnet 79a, 79b may correspond to a magnet that can rest on the region or otherwise be fastened to the region. In some configurations, a magnet can be moved along and/or away from the region to control the location and strength of the magnetic field in the region. In other configurations, magnet 79a, 79b is an electromagnet. The electromagnet may he manually and/or mechanically operated or controlled by a computer, for example as a part of an automated system. For example, analysis and sorting system 10 may be computer controlled. As a part of the automated process, the strength and/or duration of the magnetic field may be controlled. The electromagnet composition and/or structure is not particularly limited. The electromagnet may be made of any suitable material such as a magnetic core of iron, cobalt, nickel, and/or steel. The composition of the electromagnet may be configured to desired applications. Some materials may produce a stronger magnetic field. In the presence of a magnetic field in second separation region 78, magnetically labeled biological materials may be sequestered in second separation region 78. Other methods of separation may be readily adapted in lieu of or in addition to magnetic separation, for example separating target biological materials labeled with buoyant separation entity such as beads. In such configurations, magnet 79a, 79b may not be present.

[0099] In the presence of a magnetic field in second separation region 78, magnetically labeled biological materials may be sequestered or have their flow⁷ impeded in second separation region 78. Given that unlabeled and/or unbound biological materials as well as other nontargeted components of the fluid stream unimpeded in first separation region 71 may have already flowed through the remainder of analysis and sorting system 10, second separation region 78 may receive, from mixing region 76, a fluid flow containing a mixture of purified, magnetically labeled target biological materials that may have been first impeded or sequestered in first separation region 71 and any reagent, sample, or fluid components received by mixing region 76 from reagent reservoir 74. Some of the magnetic species may be capture complex 601 that has not experienced cleavage, and/or a cleaved portion of capture complex 601 that includes capture complex separation entity 670 and cleaved capture complex linker 660. The magnetic species may also be cleaving complex 602. Preferably, the sequestered magnetic species include both cleaving complex 602 and a cleaved portion of capture complex 601 that includes capture complex separation entity 670 and cleaved capture complex linker 660. Therefore, second separation region 78 may separate, sequester, or impede anything bound to cleaving complex separation entity 630 and/or capture complex separation entity 670. Accordingly, capture complex separation entity 670 with capture complex linker 660 and cleaving complex separation entity 630 linked to cleaving entity 610 may be the same or different separation entities with the same or different labeling and/or magnetic properties. Preferably, capture complex separation entity 670 with capture complex linker 660 and cleaving complex separation entity 630 linked to cleaving entity 610 may be configured for simultaneous separation from other components in the mixture, by the same separation mechanism or mechanisms. More preferably, cleaving complex separation entity 630 and capture complex separation entity 670 may be the same separation entity. Cleaving complex 602 may be sequestered in second separation region 78. Some or all of cleaved capture complex linker 660 still linked to capture complex separation entity 670 may be retained in second separation region 78. The target biological materials may be released from capture complex separation entity 670 by cleaving entity 610 in mixing region 76, in mixing region to second separation region line 77, and/or in second separation region 78.

[0100] The magnetically labeled species in second separation region 78 of Fig. 1 A and IB may be sequestered or have their flow impeded in the presence of a magnetic field that acts on magnetically labeled species. Similarly, separation entities used in other separation mechanisms such as buoyancy beads may sequester, impede, and/or divert the flow of these labeled species through second separation region 78. Magnetic species that enter second separation region 78 may include magnetic separation entity, magnetic separation entity linked to a binding entity, magnetic separation entity linked to a binding entity which is bound to target biological materials, and/or cleaving entity linked to a magnetic separation entity. Preferably, in second separation region 78, capture complex 601 including target biological materials would have been cleaved to release the target biological materials prior to entering second separation region 78. In the second separation region, target biological materials 661 that were cleaved from capture complex separation entity 670 at capture complex linker 660 by cleaving entity 610 in either mixing region 76, mixing region to second separation region line 77, and/or second separation region 78, may be released to flow to analysis and sorting device 23. Because unbound fractions may have already flowed through and/or may have been removed from analysis and sorting system 10 in first separation region 71, at least 90, 91, 93, 95, 96, 97, 98, 99, 99,5, 99.8%, or more of the biological materials remaining from the original sample in second separation region 78 may be target biological materials. In second separation region 78, therefore, target biological materials may be significantly enriched and released from the separation entity by having already been cleaved in either mixing region 76 or mixing region to second separation region line 77, and/or being near the cleaving entity in second separation region 78. For example, in the presence of a magnetic field in second separation region 78, magnetic separation entity, magnetic separation entity linked to a binding entity, and/or the cleaving entity which is linked to magnetic separation entity may remain, while significantly enriched target biological materials released from capture complex separation entity 670 may flow to analysis and sorting device 23 without any remaining labeling by separation entity from the separation mechanism.

[0101] In some configurations where magnetic separation is employed, second separation region 78 may include one or more magnets 79a, 79b. In some configurations, magnets 79a, 79b may be presented in a variety of patterns. For example, Figs. 1 A and 1 B illustrate magnets 79a, 79b at the relative top and bottom of second separation region 78. However, magnets 79a, 79b may correspond to columns that extend into the interior of second separation region 78. Such a configuration may be desirable to ensure the capture of magnetic separation entities and/or magnetically labeled biological materials, and/or to affect the flow rate of sample and/or fluid through at least second separation region 78. The likelihood of capture by the magnetic field may be increased by increasing the duration of the sample and/or fluid in second separation region 78. The magnitude of the magnetic force exerted upon the magnetic separation entities and/or magnetically labeled biological materials, the flow rate, and/or the shape, dimensions, and/or structure of second separation region 78 may be configured to immobilize or impede the progress of labeled species through second separation region 78. [0102] Magnets 79a, 79b may generate a magnetic field or a magnetic field gradient. In some configurations, one magnet 79a, 79b may have an opposite polarity of the other magnet 79a, 79b so that magnetic species can be repelled, moved, or pushed towards the other magnet 79a, 79b. For example, a magnetic field of one polarity generated by magnet 79b in second separation region 78 may be sufficient to drive magnetically labeled species towards the other magnet 79a of the opposite polarity. Both magnets may be located on the exterior and/or interior of second separation region 78, and/or be integral with second separation region 78. Magnetic forces that act upon each magnetic species may be related to magnetic separation entity size and/or geometry .

[0103] During wash processes, the structure and/or dimension of second separation region 78 may be constructed to make it more difficult to shear target biological materials bound to the separation entity and/or remove or dislodge bound biological materials from the separation mechanism. Any number of wash steps may occur before, during, or after, the separation mechanism (e.g., a magnetic field) is activated or present. In some configurations, a washing process may occur constantly or in parallel with the separation mechanism due to a constant flow of provided buffer, media, or other fluid through analy sis and sorting system 10. The wash steps may remove unbound biological materials (i.e., those not sequestered by the separation mechanism) such as those not having a magnetic label, unincorporated reagents such as binding entities not linked to a magnetic label, as well as biological materials in the sample that are not bound to a labeling entity either directly or via an intermediary? such as a binding entity. Wash steps can also facilitate flowing the target biological materials through second separation region 78 in the fluid stream to analysis and sorting device 23. In the presence of the magnetic field, for example, magnetically labeled target biological materials may be immobilized, thereby facilitating cleaving by the cleaving entity, which may release or separate the biological materials from the magnetic separation entities in the sample and/or fluid provided to second separation region 78 from mixing region 76. Additionally, cleaved magnetic separation entities may remain in second separation region 78, providing target biological materials devoid of magnetic separation entities to analysis and sorting device 23. [0104] Second separation region 78 may be composed of any suitable material such as glass, thermoplastic, flexible tubing, silicon, elastomer, etc. It may be coated with any material and may be functionalized as is known in the art. Second separation region 78 may also be functionalized by embedding or reinforcing its majority composition material with another material to impart certain separation properties to the region. For instance, in the case of magnetic separation, the region may be composed of a majority of an above material embedded with another material, such as particles or wires of the aforementioned metals, suitable to impart magnetic properties to the region. The thickness of the material is also not particularly limited. Thickness of the material may affect for example, penetration of a magnetic field into second separation region 78. The sample and/or fluid may flow generally from left to right through second separation region 78 as illustrated in Figs. 1 A and IB. In some configurations, the direction of flow may be reversed. The rate and direction by which sample and/or fluid flows through the region may be controlled by one or more pumps. The biological materials and separation entities may experience gravity as a function of their mass and density. Thus, in the case of magnetic separation, the flow rate, the strength of the magnetic field, and composition and/or conformation of the magnetic and/or magnetically labeled biological materials and separation entities may be selected to ensure that the magnetic species are immobilized or impeded by magnets 79a, 79b. The flow rate may be selected to ensure that the biological materials and separation entities do not sediment or rest at the bottom of a line and/or second separation region 78 in some configurations. In the case of labeling target biological materials with buoyancy beads, however, it is desirable that the beads float towards the top of second separation region 78. The efficiency of separation may allow for the separation of single biological materials based upon the label, biological material size/shape, separation entity size/shape, magnetic field strength, flow rate, and size/ structure of second separation region 78.

[0105] Second separation region 78 is not particularly limited by its shape. The shape may affect the flow rate of sample and/or fluid. For example, a larger volume may decrease the flow through second separation region 78. In some configurations, the second separation region 78 corresponds to a position along a length of tubing in which a magnetic field is applied, and/or where the tubing is functionalized as described above. The shape of the tubing may be indistinguishable from tubing before and after the second separation region 78. Second separation region 78 may accommodate any number of inlets 91c, outlets 93c, and/or magnets 79a, 79b or other structures suitable for different separation mechanisms. The location of inlets 91c, outlets 93c, and/or magnets 79a, 79b or other structures is not particularly limited. Magnets 79a, 79b may follow a contour or portion of a contour of second separation region 78. The shape and/or volume of second separation region 78 can affect the flow rate of sample and/or fluid through the separation region to an outlet. Volume can be inversely proportional to the flow rate. The effect of volume on flow rate can be further modified by including, for example, a pump to the system. Some such configurations are disclosed in U.8. Pat. No. 10,240,186, the contents of which are incorporated herein by reference.

[0106] As noted above, analysis and sorting system 10 may include multiple separation regions, mixing regions, and/or analysis and sorting devices in parallel and/or series including some or all of the other components illustrated in Figs. 1 A and IB. Analysis and sorting system 10 may, for example, measure and sort multiple parameters at once, like in conventional FACS, but unlike in conventional MACS or MIC S Figs. 7A-7E show one example of mixtures to be contained and target biological materials to be separated based on multiple parameters in a series of separation regions and mixing regions. In Fig. 7A, labeled target biological materia! 201 expressing multiple different markers 202, 203 is illustrated, prior to any relevant separation, along with labeled biological material 210 expressing only marker 202 and unlabeled biological material 211 expressing only marker 203. Markers 202, 203 can be, for example, proteins, carbohydrates, or other molecules which indicate a biological material to be separated. In some embodiments, the markers 202, 203 can be proteins on the surface of a ceil as the biological material 201. Each label at this stage includes, similar to capture complex 601, a first capture complex of first capture complex separation entity 204 which are linked, through a first capture complex cleavable linker 205, to first capture complex binding entity 206, which has an affinity for marker 202 expressed by target biological material 201 and biological material 210, but not. by biological material 211. Target biological material 201, along with biological material 210, both of which express marker 202, may be sequestered in a first separation region based on their labeling with first capture complex separation entity 204. For example, target biological material 201 and biological materi al 210 may be sequestered based on magnetic sorting, if first capture complex separation entity 204 are magnetic beads. Biological material 211 not expressing marker 202, and therefore also not labeled with any separation entity, may be washed through the system and discarded. Thus, the remaining mixture then contains the captured components shown in Fig. 7A, without biological material 211 expressing only marker 203 since it was not iabeled/captured and was washed away. Subsequently, the labeled target biological material 201 and biological material 210 expressing marker 202 in the first separation region may be released to a first mixing region. In the first mixing region, components as shown in Fig. 7B are added: similar to cleaving complex 602, a first cleaving complex 207 including first cleaving complex separation entity 208 linked to a first cleaving entity 209 that recognizes first capture complex cleavable linker 205 of Fig. 7 A, and a new label including second capture complex separation entity 224 which are linked, through a second capture complex cleavable linker 225, to second capture complex binding entity 226, which has an affinity for marker 203. At this stage, target biological material 201 and biological material 210 expressing only marker 202 may be released from first capture complex separation entity 204 by the action of first cleaving entity 209. Remaining target biological material 201 also expressing marker 203 may then be labeled by second capture complex separation entity 224 which are linked, through second capture complex cleavable linker 225, to second capture complex binding entity 226 that recognizes marker 203. The result of the action of first cleaving entity 209 and the binding between second capture complex binding entity 226 and marker 203 may be as the mixture shown in Fig. 7C, wherein first cleaving complex 207 also remains, along with cleaved first capture complex separation entity 204 and cleaved biological material 210. The mixture in Fig. 7C may then be released to a second separation region. In the second separation region, the target biological material 201 expressing marker 203 may be sequestered if they are bound to second capture complex separation entity 224, alongside cleaved first capture complex separation entity 204 and first cleaving complex 207. Biological material 210 not expressing marker 203, and therefore unlabeled at this stage, may be washed through the system and discarded, even though they express marker 202. Subsequently, the labeled target biological material 201 expressing marker 203 in the second separation region may be released to a second mixing region. In this example, components still linked to first capture complex separation entity 204 and first cleaving complex separation entity 208 would also be released to the second mixing region, along with labeled target biological material 201, In the second mixing region, a component as shown in Fig. 7D is added: a second cleaving complex 227 that has second cleaving complex separation entity 228 linked to second cleaving entity 229 that recognizes second capture complex cleavable linker 225. Second cleaving entity 229 recognizing second capture complex cleavable linker 225 may release target biological materia! 201 from second capture complex separation entity 224, resulting in the mixture shown in Fig. 7E. This mixture may be released to a third separation region, which can sequester first capture complex separation entity 204, first cleaving complex separation entity 208, second capture complex separation entity 224, second cleaving complex separation entity 228, and anything bound thereto. The remaining target biological material 201 expressing both markers 202, 203, now unlabeled by capture complexes, may flow out of the third separation region without any of the other components shown in Fig. 7E, all of which are linked to one of first capture complex separation entity 204, first cleaving complex separation entity 208, second capture complex separation entity 224, or second cleaving complex separation entity 228. Thus, only target biological material 201 expressing both markers 202, 203 are provided at the end of the process as depicted in Figs. 7A-E. Other biological material 210, 211 that do not express both markers 202, 203 would have been already separated from target biological material 201 and washed through the system to be discarded or collected. In addition, the labels first capture complex separation entity 204 and second capture complex separation entity 224, and first cleaving complex 207 and second cleaving complex 227, all used to select for target biological material 201, are also separated from target biological material 201, having been captured in the third separation region. Such a process and configuration may be implemented for different types of target biological materials.

[0107] The above-described system and substantially similar systems can be used in a method for the selection and separation of different components within a sample.

[0108] An example of a method of separating, enriching for, and/or analyzing target biological materials is provided in Fig. 8. At 810, a first mixture that includes target biological materials, and a second mixture that includes a cleaving complex, may be received by the mixing region. For example, the first mixture may be provided to the mixing region from the first separation region via a line. The first separation region may contain a mixture of labeling separation entity, a binding entity such as an antibody that recognizes a marker such as an antigen of a biological material, and biological material. In some configurations, the probe may provide a mixture to the first separation region that includes separation entity, binding entity, and biological material In some configurations, the separation entity, binding entity, and biological material may be provided separately to the first separation region such as via separate lines and/or separate wells. In general, the components of the first mixture can preferably form a complex that includes separation entity linked directly or indirectly to the binding entity, which in turn are bound to target biological material.

[0109] Sample and/or fluid may be drawn into the first separation region by the probe. The sample is not particularly limited. In some embodiments, at least a portion of it may be labeled, preferably prior to collection with probe 11. in some preferred embodiments involving labeling, the sample includes a labeled biological material or materials and/or unlabeled biological material or materials. The labeled and/or unlabeled biological material or materials may each independently include one or more cells, cell fragments, viruses, virus fragments, exosomes or extracellular vesicles and fragments thereof, proteins, nucleic acids, or carbohydrates. Proteins, if present, can include a protein complex, a multiprotein complex, a single polypeptide, an oligopeptide, or any combination thereof. Nucleic acids, if present, can include chromosomes, polynucleotides, oligonucleotides, a nucleic acid complex, or any combination thereof Carbohydrates can include, for example, sugars, oligosaccharides, polysaccharides, a carbohydrate complex, or any combination thereof. The sample preferably includes one or more biological materials such as cells, which in some embodiments may be immune ceils, stem cells, or circulating tumor cells (CTCs). Examples of immune cells that may be included in the sample include leukocytes such as T ceils, B cells, natural killer { N K ) cells, dendritic cells, monocytes, and macrophages. Native or engineered T cells are preferred as leukocytes in certain embodiments, and may include tumor-infiltrating lymphocytes { 1 11.s). T cells including one or more chimeric antigen receptor proteins, or T cells including one or more T cell receptor proteins suitable for the diagnosis or treatment of cancer, infectious diseases, or autoimmune diseases. In other embodiments, the leukocytes may include native or engineered B cells, in particular engineered B cells suitable for the diagnosis or treatment of cancer, autoimmune diseases, infectious diseases, or protein deficiency diseases. In still other embodiments, the leukocytes may be native or engineered NK ceils, for example NK cells including a chimeric antigen receptor protein, in particular those suitable for the diagnosis or treatment of cancer, infectious diseases, or autoimmune diseases. In further embodiments, the leukocytes may be native or engineered dendritic cells, for example engineered dendritic cells suitable for the diagnosis or treatment of cancer, infectious diseases, inflammatory diseases, degenerative diseases, autoimmune diseases, and organ transplantation. In still further embodiments, the leukocytes may be native or engineered monocytes, for example engineered monocytes suitable for the diagnosis or treatment of cancer, infectious diseases, inflammatory_' diseases, degenerative diseases, autoimmune diseases, and organ transplantation. In other embodiments, the leukocytes may be native or engineered macrophages, for example engineered macrophages suitable for the diagnosis or treatment of cancer, infectious diseases, inflammatory diseases, degenerative diseases, autoimmune diseases, and organ transplantation. Stem cells may include, for example, embryonic stem cells, neural stem cells, mesenchymal stem cells, hematopoietic stem cells, or induced piuripotent stem cells (iPSCs). Embodiments with a sample including stem cells may include stem cells suitable for genetically engineered correction of a disease or condition, or for transplantation. The stern cells, if present, may be suitable for the treatment of neurodegeneration, diabetes, multiple sclerosis, cerebral palsy, macular degeneration, cardiovascular diseases, or musculoskeletal diseases. CTCs may include, without limitation, tumor cells released from a solid or primary tumor into the surrounding vasculature or lymphatic system to then circulate in the bloodstream, CTCs may be suitable for the detection and diagnosis of cancer. Where the sample includes cells, the cells may be bacterial cells, plant cells, yeast or fungal cells, or animal cells. In certain embodiments, the cells are preferably engineered or native animal cells, and in particular embodiments, the cells are more preferably engineered or native human ceils. The labeled and unlabeled biological material or materials may be naturally- occurring, or may be modified from their native states for example by mutation or genetic engineering, or may be a combination of both types of materials. In some preferred embodiments, the sample includes at least one modified and labeled biological material, preferably including one or more modified and labeled cells.

[0110] In some preferred embodiments, the sample has been originally or initially obtained from a subject. The subject may be a human subject, another organism, or a blood or tissue sample, preferably a human subject or a human blood or tissue sample. The subject may preferably be a patient in need of treatment, or in other embodiments, the subject is a different individual from a patient in need of treatment. The sample may be initially obtained from the subject as a blood sample or as a tissue sample, preferably as a blood sample and/or a sample obtained from a tumor, a tumor stroma, or other tissue subject to a condition in need of treatment. After the sample is initially obtained from the subject, at least one component of the blood and/or tissue may be removed or isolated as the sample. The component to be removed or isolated as the sample biological material may include one or more ceils, cell fragments, viruses, virus fragments, exosomes or extracellular vesicles and fragments thereof, proteins, nucleic acids, or carbohydrates. The component to be removed or isolated as the sample is preferably one or more cells, more preferably lymphocytes, and in particular, T cells are preferred in certain embodiments.

[0111] In some preferred embodiments, once the sample has been removed or isolated, it is modified, or it is used to modify another biological material. Modifications may include genetic engineering, including the introduction of DNA and/or RNA into a ceil in order to express a desired trait and/or produce a desired structure, preferably a protein; alternatively, the modifications may have the goal of removing or inhibiting the expression of a desired trait and/or production of a desired structure. In certain preferred embodiments, the removed or isolated sample includes T cells, and the modification includes providing the T cells with DNA which encodes for one or more receptor proteins. In these embodiments, the receptor protein can be a T cell receptor or chimeric antigen receptor configured to selectively bind to one or more tumor cell antigens. In some embodiments, the receptor protein is an anti-CD 19 chimeric antigen receptor.

[0112] In some embodiments related to TIL adoptive ceil therapy, the sample may be initially obtained from the blood or a tumor from a patient in need of treatment. The sample may be sorted to separate TILs, such as T cells, and tumor ceils. In some embodiments, separated T cells may be further isolated as individual single cells. T cells are expanded ex vivo and then exposed to the tumor cells to identity T ceils that react against the tumor cells. In some embodiments, the reactive T cells may be identified and selected for reactivity' by the presence of cell surface proteins, such as but not limited to CD137/4-1BB, CD 134/0X40, and/or CDI07a/LAMP-l . T cells that indicate as reactive to the tumor cells may be selected and further expanded to be infused back into the patient with IL-2 treatment to promote expansion and engraftment.

[0113] In some embodiments, the sample includes reagents or particulate components, which may be suitable for analysis and/or sorting, or for facilitating an analysis and/or sorting method. Reagents or particulate components can include separation entities such as beads. Such reagents or particulate components may be present in the sample instead of, or in addition to, a biological material. In some embodiments, the reagents or particulate components are provided with one or more biological materials. For example, a surface of a bead may be provided with a binding entity such as an antibody, in particular an antibody configured to capture cells or other biological materials. The reagents or particulate components, for example beads, may include a label, for example a fluorescent or magnetic label. Such a label may be provided within the beads and/or on a surface of the beads, either directly or via a linking group. In some configurations, the sample and reagents (e.g, beads and/or antibody) may be mixed and incubated together prior to intake into the first separation region. In some configurations, the sample and reagents may be separately taken into the first separation reagent in parallel, such as via separate lines, and/or in series, such as input of one component followed by input of another component (e.g., sample and/or reagent).

[0114] To facilitate analysis, separation, selection, and/or sorting, the biological material may be labeled, preferably in a selective manner, and preferably prior to collection with probe 11. The label may be a chemical, isotopic, magnetic, or fluorescent type label. In some embodiments, the label preferably includes a label which is suitable for detection in an optical manner, in particular a fluorescent label, for example phycoerythrin (PE) or carboxyfluorescein succinimidyi ester (CFSE), or fluorescent proteins such as enhanced GFP (eGFP), or nanoparticles such as quantum dots. The label can also include a magnetic label, instead of an optical label, or in some preferable embodiments in addition to an optical label. If the labeling is selective, then the selective labeling may be selective for the presence of target biological material, such as a for a protein or receptor marker on the surface of a cell in the sample, for example a T ceil receptor or chimeric antigen receptor capable of binding to one or more tumor cell antigens, such as an anti- CD19 chimeric antigen receptor. In other embodiments, the labeling may be selective for the presence of surface protein markers that, indicate an activated or reactive T cell, for example,

CD 137/4- IBB, CD 134/0X40, and/or CD107a/LAMP-l. A label may include one or more labels for different characteristics and/or markers, such as for the presence of different proteins, or for the presence of a protein and another characteristic. In such a plurality of labels, the labels may be the same or different. Labels of the same type may be used for selecting for multiple traits with the same type of analysis and sorting method, for example in the embodiment depicted in Figs. 7A-7E.

[0115] In the embodiment of probe 11 as shown in Figs. 3 A, 3B, and 4, to obtain the sample in the open end 102 of probe 11, a fluid may be provided from fluid supply 104. The fluid is preferably a liquid, more preferably a saline solution, even more preferably a buffered saline solution. The buffer, if present, may be a phosphate buffer. In some embodiments, the fluid is a fluid suitable as a sheath fluid for flow cytometry, or a fluid which can be combined with one or more other substances to provide a sheath fluid for flow cytometry. In other embodiments, the fluid is a ceil culture medium. Preferably, the fluid itself as provided through fluid supply 104 to open end 102 is suitable as a sheath fluid for flow cytometry. In some configurations, such as where probe 11 is a pipette or a syringe, fluid may be drawn into the probe from a sample well, tube, or the like, and conveyed to the first separation region.

[0116] The fluid may be provided to fluid supply 104 by pumping, for example with a probe input pump 41. In preferred embodiments, the flow rate of the fluid through fluid supply 104 to open end 102 is regulated, which may include measuring with a flow meter and/or regulating the flow rate with a flow regulator. The flow rate of the fluid through fluid supply 104 to open end 102 is, in some embodiments, also a volumetric flow rate suitable for flow cytometry. In such embodiments, the flow rate may be from 10 to 1,000 pL/min, in particular from 10 to 20 pL/min or from 100 to 1,000 pL/min. The flow rate of the fluid through fluid supply 104 to open end 102 may be greater than, substantially the same as, or identical to a flow rate for removing a fluid stream from open end 102 of probe 11 through fluid exhaust 105. In some embodiments, the flow rate of the fluid through fluid supply 104 to open end 102 is from 1% to 10% greater than a flow rate for removing a fluid stream from open end 102 of probe 11 through fluid exhaust 105, more preferably about 5% greater. By maintaining a sufficient flow rate through fluid supply 104 to open end 102 so as to replace at least the fluid removed through fluid exhaust 105, probe 11 in analysis and sorting system 10 and the method of using it can avoid the intake of air or other gas into fluid exhaust 105, thereby avoiding the undesired presence of gas into flow cytometer 20 or analysis and sorting device 23.

[0117] Accordingly, in some embodiments, in order to avoid the undesired presence of gas in flow cytometer 20 or analysis and sorting device 23, a device or devices like probe 11 may be included between a mixing region and a separation region, between mixing regions, or between separation regions. In particular, if a mixing or separation method may involve some introduction of air or another gas into a mixture containing a sample, then afterward, the sample may be processed through a probe-like structure which maintains a sufficient flow rate through fluid supply 104 to open end 102 so as to replace at least the fluid removed through fluid exhaust 105. The probe-like structure can therefore he used to avoid the intake of air or other gas into a sample to be provided to a flow cytometer or analysis and sorting device.

[0118] Upon arrival at open end 102 of probe 11, the fluid may form a fluid dome 107 as shown in Fig. 4. A sample may enter open end 102 by contact with fluid dome 107. In some embodiments, the sample may enter fluid dome 107 when fluid dome 107 contacts a sample, for example a sample as such or an aqueous suspension or dispersion of the sample, in a sample container or containers such as tubes, flasks, or a well 51 of a well plate 50. In other embodiments, the sample could be provided to open end 102, preferably having dome 107, by the provision of drops or sprays of the sample to open end 102. For example, some embodiments of the method may convey sample to open end 102 of probe 11 with an automated pipetting system, or by directing acoustic energy into the samples within individual wells to eject droplets of the sample toward open end 102 of probe 11. In some such embodiments, for example where the wells or other sample container or containers are sufficiently narrow so as to retain the sample by forces such as surface tension or adhesion even in other orientations, open end 102 of probe 11 may point in an upward direction, a sideways direction, or at a skew angle with respect to a vertical direction. In some such embodiments, an upward direction for the probe and an inverted orientation of the sample container or containers may be particularly preferred. In some cases, sample and/or fluid may be drawn into the probe without formation of a dome. [0119] A fluid stream including the fluid and the sample may be removed from open end 102 through fluid exhaust 105 by pumping, for example with a pump. In preferred embodiments, the flow rate of the fluid stream through fluid exhaust 105 out from open end 102 is regulated, which may include measuring with a flow meter and/or regulating the flow rate with a flow regulator. This flow rate may additionally or alternatively be regulated based on data from a sensor, for example a light-based sensor, which can monitor the size, curvature, or other parameters of dome 107 to provide data for maintaining optimal flow into or out of probe 11. The flow rate of the fluid stream through fluid exhaust 105 away from open end 102 is, in some embodiments, also a volumetric flow rate suitable for flow cytometry'. In such embodiments, the flow rate may be from 10 to 1,000 pL/niin, from 10 to 20 pL/min, or from 100 to 1,000 pL/min. The flow rate of the fluid stream through fluid exhaust 105 out from open end 102 may be less than, substantially the same as, or identical to a flow rate of the fluid through fluid supply 104 to open end 102. In some embodiments, the flow rate through fluid exhaust 105 out from open end 102 is from 1% to 10% less than a flow rate through fluid supply 104 to open end 102, more preferably about 5% less. By maintaining a sufficiently low flow rate through fluid exhaust 105 so as to prevent the intake of gas or air along with the sample and the fluid supplied through fluid supply 104 to open end 102, probe 11 in analysis and sorting system 10 and the method of using it can avoid the intake of air or other gas into fluid exhaust 105, thereby avoiding the undesired presence of gas into flow cytometer 20 or analysis and sorting device 23. A flow rate through other components of the apparatus may be from 10 to 1,000 mΐ,/min.

[0120] The fluid stream removed from open end 102 of probe 11 through fluid exhaust 105 of probe 11 may be conveyed to first separation region 71. As provided earlier, one or more of the lines in analysis and sorting system 10 may be free of joints, junctures, or valves in some embodiments; in other embodiments, the lines may include at least a joint, juncture, or valve. Preferably, the presence of gas in the fluid stream may be avoided. Therefore, some embodiments may lack a joint, juncture, or valve in any individual line or in all lines. In other configurations, one or more of the first separation region, the second separation region, and/or the mixing region may have valves that can be opened or dosed to allow fluid to pass through. For example, during a washing step, rather than pass wash fluid through the entire sorting system, a valve may be opened to shunt wash fluid to a separate path to be discarded.

101211 As the fluid stream is conveyed from open end 102 of probe 11 through fluid exhaust 105 of probe 11 to first separation region 71, the fluid stream may or may not receive or be joined by an additional component or components. In some embodiments, the fluid stream travels without added components to first separation region 71. In other embodiments, the fluid stream may be diluted with water, or an optionally-buffered saline solution may be added. For example, the fluid stream may include separation entity, binding entity, sample, and/or fluid. In other embodiments, one or more labels of the same or different types may be added to the fluid stream, for example a fluorescent label, a binding entity linked to a separation entity, a cleaving entity linked to a separation entity, or any other suitable label for biological materials.

[0122] Once in first separation region 71, the components of the fluid stream may in some embodiments be separated. For example, in some configurations, the first separation region employs magnets to attract magnetic separation entities such as beads or magnetically labeled biological materials to particular structures located within the interior or to the inner side of the exterior portion of the first separation region. In some configurations, the first separation region may separate components based upon a different principle such as buoyancy and/or sedimentation.

[0123] For example, buoyancy beads such as glass microbubbles may be used as a separation entity and linked to a target-specific binding entity such as an antibody, and may be mixed with biological materials. U.S. Pat. App. Pub. No. 2016/0167061 discloses methods for sorting cells using buoyancy beads/microbubbles. Upon mixing, the target biological material bound to the antibody may float to the top of a solution. The beads for buoyancy are not particularly limited. For example, they may have an average diameter of 10-20 pm such as the ΪM30K glass microbubbles from 3M™ In configurations using buoyancy beads, the first separation region may not include magnets, and may have a mechanism to facilitate mixing, rocking, or centrifugation. The buoyancy beads may cause the target biological material bound by the antibody, which is in turn linked to the bead, to rise to the top of the region. The first separation region may have outlets that draw or siphon sample and/or fluid from the top of the region. In some instances, beads near the top of the region may be homogenized with the volume of liquid in the first separation region before being allowed to proceed to the mixing region. For example, the mixture in the first separation region may be agitated and mixed by an active or passive stirring mechanism or by the addition of fluid from the top of the region.

[0124] In still another embodiment, separation may be based upon the sedimentation of separation entity such as beads labeled with a target-specific binding entity. Sedimentation may utilize gravitational force or other forces such as a centrifugal force acting on beads. Fluid may be passed over the sedimented beads in the first separation region or through the first separation region to remove undesired material or wash sedimented components. The washing fluid or undesired components may be washed through analysis and sorting system 10 to prevent contamination of the desired components. Sedimented beads may be conveyed to the mixing region by agitating the separation entities or rotating the first separation region to resuspend them in fluid and convey the fluid containing the separation entities to the mixing region.

[0125] In the first, separation region, target biological material may be separated from nontarget biological materials as well as other components that are not bound to a capture or separation entity such as a bead. The target biological material may be retained in the first separation region by being labeled/bound to a separation entity via a binding entity intermediary such as an antibody, for example, to form a capture complex. In some configurations, the flow of the capture complex through the first separation region may be impeded or completely immobilized because of its label relative to biological materials that are not targeted or of interest because of their lack of labeling. One or more washes may be performed of the capture complex by conveying fluid through analysis and sorting system 10, in particular, through the first separation region. The complex may be released to the mixing region in any number of ways. For example, where the separation entities (e.g., beads) of the capture complex are magnetic, the presence of the magnetic field may be reduced or removed, thereby allowing the capture complex to flow through to the mixing region and/or through the remainder of analysis and sorting system 10. In the case where the separation entities of the capture complex are buoyancy beads, the capture complex may be removed or siphoned from the first separation region via one or more outlets at the top of the region. Alternatively, or in addition thereto, the beads may be resuspended in the fluid of the region by gentle agitation or rotation. In some configurations, the region may have a shape that facilitates collection of the beads near the top such as a cone shape or a rectangular shape where the flow is significantly reduced. In such configurations, fluid may be applied to the top of the region to force the beads of the capture complex to reenter a main part of the region so that they are carried to the next region (i.e., mixing region). A similar principle may be applied where the separation entities are sedimentation beads that are a part of a capture complex, except that the shape to collect or sequester the beads out of the fluid stream may be at the bottom of the region and fluid may be applied from the bottom of the region, or the beads may be resuspended in the fluid of the chamber by gentle agitation or rotation.

[0126] From the first separation region, therefore, the capture complex, which may constitute at least a portion of the first mixture, may be conveyed to the mixing region via one or more inlets from one or more lines. In the mixing region, reagent may be received from the reagent reservoir. The reagent may include, for example, a buffer, water, or other suitable solution or fluid, as well as a cleaving complex and/or additional capture complex. The mixing region may receive a second mixture that includes the cleaving entity linked to separation entities (e.g., beads). The complexes may be labeled as described earlier, such as a magnetically. The beads may alternatively be buoyancy beads such as the glass microbubbles described earlier.

[0127] Fig. 6 shows an example of a cleaving complex 602 that can include a cleaving entity 610 coupled to a cleaving entity linker 620, which is coupled to a cleaving complex separation entity 630. Fig. 6 also shows an example of a capture complex 601 that includes a target biological material 661, a capture complex binding entity 650, a capture complex linker 660, and a capture complex separation entity 670. Capture complex linker 660 of capture complex 601 may include a capture complex cleavage site 665.

[0128] Cleaving complex linker 620 and capture complex linker 660 containing capture complex cleavage site 665 may be any protein or polypeptide, carbohydrate or polysaccharide, or nucleic acid. In some configurations, the linker includes at least 2, 4, 6, 8, 10, 12, 14, 15, 20, 25, 30, 35,

40, 45, 50, 60, 70, 80, 90, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, or 1000 amino acids. In some configurations, the linker includes at least 2, 4, 6, 8, 10, 12, 14, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, or 1000 polysaccharide residues. In some configurations, the linker contains at least 4, 10, 20, 40, 50, 80, 100, 150, 200, 300, 400, 500,

700, 800, 1000, 1250, 1500, 1750, 2000, 2500, 3000, 3500, 4000, or 5000 nucleotides. The length of the linker can depend upon how much freedom of movement is desired for the cleaving entity or how much access to capture complex cleavage site 665 is desired. If the linker is too long, it may increase shearing on the capture complex or cleaving complex, or allow too much flexibility for the cleaving entity and cleavage site, leading to interference. If the linker is too short, access to capture complex cleavage site 665 of capture complex 601 may be reduced or unavailable for cleaving entity 610. Similarly, if cleaving complex linker 620 is too short, cleaving entity 610 may not be able to act on capture complex 601 to cleave capture complex cleavage site 665 because it is not flexible enough to reach the cleavage site. In some configurations, capture complex linker 660 may be enzymatically cleaved. Examples of enzymatically releasable detection moieties are described in U.S. Pat. No. 10,197,561 and U.S. Pat. App. Pub. No. 2018/0164296. For example, the capture complex linker may be a carbohydrate or polysaccharide, protein or polypeptide, or nucleic acid that is degraded or digested enzymatically. In some configurations, the capture complex linker may be a releasable linker that does not involve an enzyme, such as streptavidin/avidin derivative and biotin derivative interactions and/or pooled weak affinity interactions. Examples of such systems are provided in U.S. Pat. No. 10,197,561, European Pat. App. Pub. No. 2725 359, or Dynabeads™ FlowComp^1M Flexi Kit, the contents of which are incorporated by reference. In the case of a biotin derivative capture complex linker, the biotin derivative may bind to streptavidin derivative-labeled separation entity. The cleaving entity may be biotin derivative that competes for streptavidin binding sites that are binding the capture complex linker, or a release buffer that alters the ability' of biotin derivative and streptavidin derivative to interact. In some configurations, the linker may be a part of a label of the separation entity. In some configurations, a binding entity such as an antibody may be modified to include the linker. Capture complex cleavage site 665 may be disposed anywhere within capture complex linker 660. For example, the cleavage site may be a six base pair DNA restriction enzyme site that is a segment or portion of a larger piece of a DNA linker, in some configurations, the entirety of the linker may be capture complex cleavage site 665. In other configurations, the linker may have multiple capture complex cleavage sites 665. For example, the cleavage site may have multiple six base pair restriction enzyme sites that are repeated contiguously or semi-contiguously in the linker. In yet other configurations, capture complex linker 660 may have multiple of the same or different cleavage sites from the same or different cleaving entities acting on the same or different linker molecules such as proteins or peptides, carbohydrates or polysaccharides, and/or nucleic acids.

[0129] Cleaving entity 610 may be an enzyme as described earlier. For example, the cleaving enzyme may be a restriction enzyme that recognizes a specific nucleotide sequence in the cleavage site of the capture complex linker. In some cases, the cleaving entity may not be site specific, but have substrate specificity, such as DNAse I, which may non-specifically cleave a DNA cleavage site or sites in the capture complex linker. In some instances, the cleaving entity may be a protease with site specificity for a sequence of amino acids found in the cleavage site of the capture complex linker. For example, the protease may be thrombin, Tobacco Etch Vims (TEV) endopeptidase, Factor Xa, or the like. In other instances, the cleaving entity may be a may be a glycosidase with site specificity for specific polysaccharide structures and/or glycosidic linkages.

[0130] Capture complex 601 and cleaving complex 602, which may constitute components of the first and second mixtures respectively, may be mixed in the mixing region using any variety' of passive and/or active methods as described earlier. The first and second mixtures may be conveyed to the second separation region. The second separation region may separate the cleaved capture complex and cleaving complex from the cleaved target biological material. Capture complex separation entity 670 of capture complex 601 that have experienced cleavage and cleaving complex separation entity 630 of cleaving complex 602 may be sequestered in the second separation region while the target biological material may be conveyed onward, i.e., to analysis and sorting device 23. As with the first separation region, cleaved capture complex separation entity 670 and/or cleaving complex separation entity 630 may be separated, sequestered, and/or impeded by the structure of the region (e.g., the dimensions or shape of the region), by a property of the separation entity, and/or by a force acting on the separation entity such a gravitational force, centrifugal force, a buoyancy of the separation entity in the capture complex and/or the cleaving complex, and/or the presence of a magnetic field where the separation entity in the capture complex and cleaving complex are magnetic. Unbound material in the second separation region, e.g., the cleaved target biological material, may flow through the second separation region to the analysis and sorting device. One or more washes with a suitable fluid such as a buffer, water, etc., may be performed to ensure that the target biological material are conveyed to the analysis and sorting device. Similarly, the sequestered separation entities from the capture complex and/or the cleaving complex may be discarded or released to the analysis and sorting device for analysis. For example, the magnetic field generated by the magnets may be reduced or removed, thereby releasing magnetically labeled separation entities into an onward fluid stream.

[0131] At 820, at least one first fraction and at least one second fraction may be collected. Fractions may be collected, for example, by the analysis and sorting device. The first fraction may he enriched for the target biological material, while the at least one second fraction may he substantially devoid of the target biological material. Because the target biological material may begin to he released from the bead component of the capture complex when the first mixture and the second mixture are mixed in the mixing region, target biological material may begin to be detected by the analysis and sorting device. In some configurations, a series of fractions (e.g., the first and/or second fractions) may be separately collected and analyzed to detect the target biological material. In some configurations, fractions of a predetermined volume are collected into one or more containers such as a well or tube. In some configurations, each fraction is analyzed in real time so that the fractions enriched for the target biological material can be readily determined. For example, there may be continuous or semi-continuous flow of fluid to the analysis and sorting device. The fractions containing the target biological material may be saved for subsequent analysis and/or use, and the remaining fractions (i.e., at least one second fractions) may be discarded. In some configurations, a flow cytometer separates the target biological material from the fluid stream for collection and discards or exhausts the fluid stream that is substantially devoid of the target biological material, while in other configurations the fluid stream devoid of the target biological material is also collected. Thus, the term collecting at 820 may refer to the separation of target biological material from a continuous or semi- continuous flow of the fluid stream. If may refer to collecting separate individual fractions as well 1.

[0132] The one or more fractions containing the target biological material may be enriched for the target biological material, meaning that the target biological material is present in a greater number and/or amount relative to other fractions collected (e.g., the one or more second fractions), in some cases, being enriched for the target biological material may refer to a measurable or detectable number or amount of biological material. For example, an enriched fraction may contain at least 90, 91, 93, 95, 96, 97, 98, 99, 99.5, 99.8%, or more of the target biological material relative to other nontarget or undesired biological material or components in the fraction, or relative to the amount of total target biological material within the original sample. In some configurations, the undesired components such as the cleaved separation entities (e.g., beads) from the capture complex and cleaving complex, wash fluid, buffer, etc. may be collected in one or more second fractions. These may be discarded or analyzed. The one or more second fractions containing the undesired components are substantially devoid or depleted of target biological material. For example, these fractions may contain less than 15%, 10%, 5%,4%, 3%, 2%, 1%, or none of the target biological material relative to the fractions enriched for target, biological material. In some cases, this relative amount may be based upon a particle count, an amount by mass, a weight %, target label intensity, etc. A determination of amount may be made using techniques well known in the art such as by absorption, mass spectrometry, a chromatograph, a cell counter, an enzymatic assay (e.g., a horse radish peroxidase-based assay, ELISA), a colorimetric assay, a fluorescent assay, or the like.

[0133] In some embodiments, the separation process may include regulation of flow of the fluid stream, preferably by hydrodynamic focusing, including generation of a sheath flow with the fluid stream including the sample in a middle portion thereof. In other preferred embodiments, the fluid flow can be regulated by acoustic focusing with ultrasonic waves to enhance generation of a sheath flow with the fluid stream including the sample in a misled portion thereof. The fluid stream can then be separated into droplets, most or all of which preferably contain one cell or other unit of the biological material, and the droplets may each be provided with a charge. A label, when present in a droplet, is then detected. Detection in some embodiments includes provision of electromagnetic energy, preferably in the form of a laser beam, to the droplets. The energy may then excite the label, preferably through fluorescent excitation. A camera or other light-detecting apparatus can then detect the presence or absence of fluorescence, thereby detecting the presence or absence of a labeled sample in the droplet. Droplets of the fluid stream can then be sorted based on the detected presence or absence of the labeled sample, including directing of the droplets to at least two containers or other receiving points such as wells in a well plate, tubes, or flasks through the charge provided to the droplets. In other embodiments, labeled target biological materials are sorted out of a fluid flow using a magnetic solenoid sorting valve into at least two containers based on the detected presence or absence of the labeled sample. By these or other methods of flow cytometry-based sorting, the sample can be separated into at least one labeled component and at least one unlabeled or differently-labeled component. In certain embodiments, labeled components may be sorted as single or individual components into individual containers. For example, if the labeled components are biological materials such as cells, single or individual ceils may be sorted into individual containers as the only labeled component within that container.

[0134] In still other embodiments, sorting by flow cytometry may include sorting the sample by microfluidic sorting into at least, two containers 61a and 61b or other receiving points as directed by the microfluidic analysis and sorting device, for example, wells in a plurality of well plates or wells in the same well plate, as shown in Fig, IB. Microfluidic sorting is not particularly limited, except in that it sorts components of a fluid stream from probe 11 based on any fluorescent, magnetic, isotopic, or chemical label or labels provided on the components, and/or based on a property or properties of the components unrelated to any label such as size, shape, density, binding capability, conductivity, or acoustic properties. Microfluidic sorting may involve regulating the fluid stream such that many or most biological materials or other components of the sample in the fluid stream are separated into distinct components based on the labels and/or properties mentioned above. In certain embodiments, components containing a given set of labels and/or properties are separated and sorted into one container 61a, while components lacking the given set of labels and/or properties are sorted into a different container 61b, as shown in the embodiment in Fig. IB. These containers can be separate wells of a well plate, for example a microplate, or separate tubes. In some embodiments, for example in embodiments that do not involve analysis or sorting based on fluorescence or any other light- or radiation-based phenomenon, a microfluidic analysis and sorting device such as flow cytometer 20 may not include a laser, in contrast with the embodiment of Fig. IB, showing laser 22.

[0135] In some embodiments, after separation in the analysis and sorting device 23, any number of analytical, engineering, or culturing techniques or methods may be applied to one or more separated components obtained from the sample. These techniques or methods may be performed on components that have been separated into fractions containing one or more particles of a separated component. For example, when the separated components are one or more biological materials such as cells, these techniques or methods may be performed on individual fractions containing one or more cells. Examples of analytical techniques or methods performed on separated components may include, but are not limited to, cell culture, microarray or DNA, RNA, or protein chip, imaging, immunocytochemistry, fluorescence in situ hybridization (FISH), PCR, RT-PCR, qPCR, qRT-PCR, genetic analysis, DNA analysis, RNA analysis, protein analysis, metabolic analysis, signaling pathway analysis, epigenetic analysis, phosphorylation analysis, and/or posttrans!ational modification analysis. Examples of engineering techniques or methods performed on separated components may include, but are not limited to, genetic engineering (e.g., cloning, RNA and/or protein expression, DNA integration such as by plasmid, virus, or transposon, the insertion, deletion, and/or substitution of one or more nucleic acids in a nucleic acid or amino acids in a peptide and/or protein, etc.), genome editing, RNAi, cellular differentiation, and/or cellular reprogramming. Examples through which these engineering and editing techniques or methods may be performed may include, but are not limited to, the use of nuclease-based systems such as CRISPR, TALEN, zinc finger nuclease, and/or derivatives thereof, the use of RNAi -based systems such as siRNA, shRNA, and/or miRNA, and/or treatment with chemical or biological factors such as small molecules, growth factors, and/or cytokines. Examples of culturing techniques or methods may include further culturing, differentiation, and/or reprogramming of separated biological material such as cells and/or viruses. [0136] In some embodiments, after separation in the analysis and sorting device 23, one or more components obtained from the sample may be prepared for administration to a subject in need of treatment. In some embodiments, where the one or more components obtained from the sample include cells, the cells may be cultivated. In addition, pharmaceutical adjuvants may be added, and certain components including the label may be removed, if desired,

[0137] In some embodiments, after separation in the analysis and sorting device 23 and in some embodiments after further preparation, one or more components obtained from the sample may be administered to a subject in need of treatment. The subject may need treatment, for example, for cancer, in particular melanoma, acute lymphocytic leukemia, ovarian cancer, colon cancer, prostate cancer, brain cancer, or breast cancer. The target biological material separated by the analysis and/or sorting system may be administered to a subject in need thereof as a part of a therapy.

[0138] The system and method may be further useful with respect to any cell-based therapies, including other aspects of T cell receptor (TCR) therapy, chimeric antibody receptor T cell (CAR-T) therapy, tumor-infiltrating lymphocyte (TIL) therapy, or any combination thereof, for example as discussed in Ping, Y. et al., “T-cell receptor-engineered T cells for cancer treatment: current status and future directions” Protein Cell 2018 9(3):254~256, the entirety of which is incorporated herein by reference.

[0139] In other embodiments, the sample may be analyzed in the analysis and sorting device and data may be collected about the presence, content, frequency, and/or distribution of components within the sample having different properties, or satisfying various parameters. In particular, the sample may be measured, and data may be collected as to the presence, concentration, and/or frequency of a labeled component, such as a labeled biological material, a labeled analysis reagent, or labeled particulate component. In some embodiments, analysis by flow cytometry may be combined with sorting by flow cytometry, as both described above. In other embodiments, analysis by flow cytometry' may occur without sorting, and the fluid stream including the sample may be discarded after analysis. [0140] Any reference in this specification to an “embodiment” means that a particular feature, structure, or characteristic described in connection with the embodiment is included in at least one embodiment of the invention. The appearances of such phrases in various places in the specification are not necessarily all referring to the same embodiment. Further, when a particular feature, structure, or characteristic is described in connection with any embodiment, it is submitted that it is within the purview of one skilled in the art to effect such feature, structure, or characteristic in connection with other ones of the embodim ents. The features of any one embodiment may be combined with features of one or more other embodiments described herein to form additional embodiments.

[0141] The foregoing description, for the purpose of explanation, has been described with reference to specific embodiments. However, the illustrative discussions above are not intended to be exhaustive or to limit embodiments of the disclosed subject matter to the precise forms disclosed. Many modifications and variations are possible in view of the above teachings. The embodiments were chosen and described in order to explain the principles of embodiments of the discloses subject matter and their practical applications, to thereby enable others skilled in the art to utilize those embodiments as well as various embodiments with various modifications as may be suited to the particular use contemplated.

REFERENCES

[0142] The following references are cited in the above description. Each of the references is hereby incorporated by reference in its entirety.

[0143] U.S. Pat. App. Pub. No. 2016/0167061 [0144] U.S. Pat. App. Pub. No. 2017/0268037 [0145] U.S. Pat. App. Pub. No. 2017/0284922 [0146] U.S. Pat. App. Pub. No. 2018/0164296 [0147] U.S. Pat. App. Pub. No. 2018/029305 [0148] U.S. Pat. No. 7,713,752 [0149] U.S. Pat. No. 8,727,132 [0150] U.S. Pat. No. 9,632,066 [0151] U.S. Pat. No. 9,885,032 [0152] U.S. Pat. No. 10,053,665 [0153] U.S. Pat. No. 10,073,079 [0154] U.S. Pat. No. 10,197,561 [0155] U.S. Pat. No. 10,240,186 [0156] Canadian Pat. App. No. CA2250746C

[0157] European Pat. App. Pub. No. 2725 359 (App. No. 13188639.2)

[0158] International App. Pub. No. WOl 996/031776 [0159] International App. Pub. No. WO2014/166000 [0160] International App. Pub. No. WO2020/010471 [0161] Legut etal., “Immunomagnetic cell sorting”, Nat. Biomed. Eng., vol. 3, pp. 759-760,

October 2019

[0162] Mair et al, “High-throughput genome-wide phenotypic screening via immunomagnetic cell sorting”, Nat. Biomed. Eng., vol. 3, pp. 796-805, October 2019

[0163] McKinnon, Katherine M., “Flow Cytometry: An Overview”, Curr. Protoc. Immunol., vol. 120: 5.1.1-5.1.11, February' 21, 2019

[0164] Miltenyi Biotec, “MACSQuant^® Tyto^® Cell Sorter, 2019

[0165] Ping, Y. et al., “T-cell receptor-engineered T cells for cancer treatment: current status and future directions” Protein Ceil 2018 9(3):254-256 [0166] “Dynabeads™ FlowComp™ Flexi Kit” https://www.thermofisher.eom/order/catalog/product/l 1061D?SID=srch-srp- 1116107/ 11061D?SID^::::srch-srp-l 1061 D retrieved June 4, 2020.

Claims

CLAIMS What is claimed is:

1. An analysis and/or sorting system, comprising: a first separation region having at least one first inlet and at least one first outlet, wherein the first separation region comprises a first mixture, the first mixture comprising a first capture complex, which comprises a first separation entity linked via a first linker to a first binding entity bound to a target biological material; a mixing region comprising: at least one second inlet for receiving the first mixture from the at least one first outlet of the first separation region and for receiving a second mixture comprising a cleaving entity linked via a second linker to a second separation entity, wherein the cleaving entity cleaves the first linker of the first capture complex; and at least one second outlet; a second separation region having at least one third inlet and at least one third outlet, the at least one third inlet receiving material from the at least one second outlet of the mixing region; and an analysis and/or sorting device that separates a mixture from the at least one third outlet of the second separation region into at least one first fraction enriched for the target biological material and at least one second fraction that is substantially devoid of the target biological material .

2. The analysis and/or sorting system of claim 1, wherein the first separation region and/or the second separation region comprises a magnet or an electromagnet, and wherein the first separation entity and the second separation entity are magnetic.

3. The analysis and/or sorting system of claim 1, wherein the first separation region and the mixing region are connected by a first line; and/or wherein the second separation region and the mixing region are connected by a second line.

4. The analysis and/or sorting system of claim L further comprising at least one probe that contacts a sample comprising the target biological material.

5. The analysis and/or sorting system of claim 1, wherein the first mixture and the second mixture are received by separate inlets of the at least one second inlets.

6. The analysis and/or sorting system of claim 1, wherein the analysis and/or sorting device comprises a flow cytometer.

7. The analysis and/or sorting system of claim 1, wherein the analysis and/or sorting device sorts the target biological materials and/or particles based upon one or more of fluorescence, mass, buoyancy, and/or magnetism.

8. The analysis and/or sorting system of claim L wherein the cleaving entity is selected from the group consisting of an endonuclease, a protease, and a glycosidase.

9. The analysis and/or sorting system of claim 1, wherein the linker is selected from the group consisting of a nucleotide linker, a peptide linker, and a carbohydrate linker.

10. The analysis and/or sorting system of claim 1, wherein the second mixture further comprises a second capture complex, which comprises a third separation entity linked via a third linker to a second binding entity, wherein the first binding entity binds to a first marker of the target biological material, and wherein the second binding entity binds to a second marker of the target biological material which is different from the first marker.

11. A method, comprising: combining a first mixture and a second mixture, the first mixture comprising a first capture complex which comprises a first separation entity linked via a first linker to a first binding entity bound to a target biological material, and the second mixture comprising a cleaving entity linked via a second linker to a second separation entity, wherein the cleaving entity cleaves the first linker of the first capture complex; and collecting at least one first fraction enriched for the target biological material and at least one second fraction that is substantially devoid of the target biological material

12. The method of claim 11 , further comprising, before contact between the first mixture and the second mixture, mixing the target biological material with a binding entity that binds to a marker of the target biological material.

13. The method of claim 12, wherein at least one of the separation entity, binding entity, and/or target biological material contains a label, wherein the label is selected from the group consisting of a fluorescent label, a magnetic label, an isotopic label, or a chemical label .

14. The method of claim 12, further comprising, in a first separation region, and after mixing the target biological material with the binding entity, separating the first separation entity complexed with the binding entity, the linker, and the target biological material from at least one selected from the group consisting of unbound binding entity, unbound linker, and unbound biological material.

15. The method of claim 14, wherein the first separation entity is magnetic and the first separation region comprises an electromagnet or magnet that attracts or repels the first separation entity.

16. The method of claim 11, wherein the cleaving entity is selected from the group consisting of an endonuclease, a protease, and a glycosidase.

17. The method of claim 11 , wherein the linker is selected from the group consisting of a nucleotide linker, a peptide linker, and a carbohydrate linker.

18. The method of claim 14, wherein a second separation region separates cleaved target biological material from the first separation entity and the second separation entity.

19. The method of claim 12, wherein the binding entity is an antibody, and wherein the marker is a surface antigen.

20. A method, comprising: combining a first mixture and a second mixture, the first mixture comprising a first capture complex which comprises a first separation entity linked via a first linker to a first binding entity bound to a target biological material, and the second mixture comprising a cleaving entity linked via a second linker to a second separation entity, wherein the cleaving entity cleaves the first linker of the first capture complex; collecting at least one first fraction enriched for the target biological material and at least one second fraction that is substantially devoid of the target biological material; and administering the target biological material to a patient.